Bujnicki lab - Publications
  • SOFTWARE
    • DATABASES
      • REPAIRtoire

        • REPAIRtoire is an online database for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. The DNA repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. In addition, a tool for drawing custom DNA-protein complexes is available online.

      • MODOMICS

        • MODOMICS is the first comprehesive database system for systems biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions (including the available protein sequence and structure data). It also provides literature information, and links to other databases. The database can be queried by the type of nucleoside (e.g. A, G, C, U, I, m1A, nm5s2U etc.), type of RNA, position of a particular nucleoside, type of reaction (e.g. methylation, thiolation, deamination, etc.), and name or sequence of an enzyme of interest. Options for data presentation include graphs of pathways involving the query nucleoside, multiple sequence alignments of RNA sequences and tabular forms with enzyme and literatiure data. The contents of MODOMICS can be accessed through the World Wide Web at http://genesilico.pl/modomics/

      • RNA Bricks

        • RNA Bricks is a database of RNA 3D structure motifs and their contacts, both with themselves and with proteins. The database provides structure-quality score annotations and tools for the RNA 3D structure search and comparison. 

      • RNArchitecture

        • RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a focus on structural similarities. The classification is hierarchical and similar to the system used in the SCOP and CATH databases of protein structures. Its central level is Family, which builds on the Rfam catalog, and gathers closely related RNAs. Consensus structures of Families are described with a reduced secondary structure representation. Evolutionarily related Families are grouped into Superfamilies. Similar structures are further grouped into Architectures. The highest level, Class, organizes Families into very broad structural categories, such as simple or complex structured RNAs. Some groups at different levels of the hierarchy are currently labeled as “unclassified”. For each Family with an experimentally determined 3D structure(s), a representative one is provided. RNArchitecture also presents theoretical models of RNA 3D structure and is open for submission of structural models by users. Compared to other databases, RNArchitecture is unique in its focus on structure-based RNA classification, and in providing a platform for storing RNA 3D structure predictions. RNArchitecture can be accessed at http://iimcb.genesilico.pl/RNArchitecture/.

          *The classification is expected to evolve as new data become available and we would like to encourage all interested parties to submit their suggestions for improvement as well as 3D structure predictions* 

    • STAND-ALONE
      • PROTMAP2D

        • Two-dimensional maps of contacts summarize interactions between amino acids in the structure. They reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of the residue contact maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. 

      • ModeRNA

        • We developed a method for 3D homology modeling of RNA structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence via either a fully automated or script-based approaches. ModeRNA is capable of handling 115 different nucleotide modifications and bridging gaps using fragments derived from an extensive fragment library.

      • RNAmap2D

        • RNAmap2D is a software tool for calculation of contact and distance maps based on user-defined criteria, and to some extent, quantitative comparison of pairs or series of contact maps and visualization of the results.

      • FILTREST3D

        • Filtrest3D is a program for discrimination of a large number of alternative models of protein structure or protein-ligand structure against a set of restraints derived from low-resolution experimental analyses (such as cross-linking, mutagenesis, circular dichrosm etc.) as well as from computational predictions (e.g. solvent accessibility, amino acid contact maps).

      • PyRy3D

        • PyRy3D is a software tool for modeling of structures for large macromolecular complexes. It uses Monte Carlo simulation to sample conformational space and to identify the best fit of complex components structures into a density map. Complex building process is based on distance restraints derived from experiments. 

      • Statistical potentialsRNA-Protein docking

        • We developed two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking: the quasi-chemical potential (QUASI-RNP) and the Decoys As the Reference State potential (DARS-RNP). Both potentials use a coarse-grained representation for both RNA and protein molecules and are capable of dealing with RNA structures with posttranscriptionally modified residues. In our tests that compared these methods to other published potentials, DARS-RNP showed the highest ability to identify native-like structures.

      • SimRNA

        • SimRNA - a tool for simulations of RNA conformational dynamics, including RNA 3D structure prediction

      • SupeRNAlign

        • SupeRNAlign is a tool for flexible superposition of RNA 3D structures. Our program implements an iterative algorithm that splits RNA structures into fragments and superimposes them using existing tools (currently R3D Align). Finally, the superimposed structures are saved to a .pdb file and a sequence alignment is generated.

      • QRNAS

        • QRNAS is an extension of the AMBER simulation method with additional terms associated with explicit hydrogen bonds, co-planarity base pairs, backbone regularization, and custom restraints. QRNAS is capable of handling RNA, DNA, chimeras and hybrids thereof, and enables modeling of nucleic acids containing modified residues. 

    • SERVERS
      • SimRNAweb

        • SimRNAweb is a web server interface to the SimRNA method for RNA 3D structure modeling method

      • MetaServer

        • The GeneSilico MetaServer is a gateway to a number of third-party methods for protein structure prediction (identification of domains, secondary structure prediction, fold-recognition, and finally, 3D model generation). Users can submit a protein sequence (or alignment) by a single click, then analyze the summary of results generated by many methods, and finally predict the protein structure according to the "consensus" approach.

      • FILTREST3D

        • This is an "alpha" version of a server for discrimination of a large number of alternative models of protein structure against a set of restraints derived from low-resolution experimental analyses (such as cross-linking, mutagenesis, circular dichrosm etc.) as well as from computational predictions (e.g. solvent accessibility, amino acid contact maps).

      • CompaRNA

        • The CompaRNA web server provides a continuous benchmark of automated standalone and web server methods for RNA secondary structure prediction. It has been inspired by the EVA and Livebench servers for benchmarking of protein structure prediction tools, which have greatly contributed to progress in the field of structural bioinformatics. The aim of CompaRNA is to assess the state of the art in RNA structure prediction, provide a detailed picture of what is possible with the available tools, where progress is being made and what major problems remain. The CompaRNA server is a valuable resource for all researchers who focus their attention on the usage and development of RNA structure prediction methods.

      • ModeRNA server

        • ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. It offers an option to search for potential templates, given the target sequence. The server also provides tools for analyzing, editing and formatting of RNA structure files. It facilitates the use of the ModeRNA software and offers new options in comparison to the standalone program.

      • MetalionRNA

        • MetalionRNA is a web server for the prediction of metal ions (magnesium, sodium, and potassium) in RNA 3D structures, based on a statistical potential inferred from the analysis of binding sites observed in experimentally solved RNA structures. The server is also capable of predicting Mg2+-binding sites for DNA structures.

      • MetaLocGramN

        • The MetaGramLocN is a method for subcellular localization prediction of Gram-negative proteins. The MetaGramLocN is a gateway to a number of primary prediction methods (various types: signal peptide, beta-barrel, transmembrane helices and subcellular localization predictors). The MetaGramLocN integrates the primary methods and based on their outputs provides overall consenus prediction. To make a prediction for your protein sequence use Submit or SOAP client In our benchmark, the MetaLocGramN performed better in comparison to other SCL predictive methods, since the average Matthews correlation coefficient reached 0.806 that enhanced the predictive capability by 12% (compared to PSORTb3).

      • RIBER/DIBER

        • Co-crystallization experiments of proteins with nucleic acids do not guarantee that both components are present in the crystal. While working as a PhD student with Matthias Bochtler, Grzegorz Chojnowski developed DIBER - a method with which to predict crystal content (DNA? protein? or both?) from the diffraction data. Now, we have together developed RIBER, which should be used when protein and RNA are in the crystallization drop. The combined RIBER/DIBER suite builds on machine learning techniques to make reliable, quantitative predictions of crystal content for non-expert users and high throughput crystallography. RIBER/DIBER requires diffraction data to at least 3.0 Å resolution in MTZ or CIF format.

      • MinkoFit3D

        • MinkoFit3D is a method for fitting macromolecular assemblies or their components into electron density maps. Our approach is based on finding “tight passages” inferred from the Minkowski sum boundary of two polyhedral surfaces of the structure and its map. Following the initial fit, either a robust brute-force or a genetic algorithm is used to build an initial assembly, and multi-body refinement is applied in direct electron density space.

      • Metadisorder

        • The GeneSilico MetaServer is a gateway to a number of third-party methods for protein structure prediction (identification of domains, secondary structure prediction, fold-recognition, and finally, 3D model generation). Users can submit a protein sequence (or alignment) by a single click, then analyze the summary of results generated by many methods, and finally predict the protein structure according to the "consensus" approach.

      • QA-RecombineIT

        • QA-RecombineIt provides a web interface to assess the quality of protein 3D structure models and to improve the accuracy of models by merging fragments of multiple input models. In the first stage (QA-mode), our server predicts the global quality of input models and provides estimates of local quality as the deviation between C-α atoms in the models and corresponding atoms in the unknown native structure. Together with the input models, these predictions subsequently become the input for the second stage (RecombineIt-mode), in which fragments predicted to be better than others are judiciously combined to generate hybrid (consensus) models. Finally, hybrid models are scored by the MQAPs implemented in the QA-mode and then presented to the user

      • NPDock

        • NPDock is a web server for modeling of protein-RNA and protein-DNA complex structures. It combines GRAMM for global macromolecular docking, scoring with a statistical potential, clustering of best-scored structures, and local refinement.

      • ClaRNA

        • ClaRNA is a new method for computational classification of contacts in RNA 3D structures. Unique features of the program are the ability to identify imperfect contacts and to process coarse-grained models. Each doublet of spatially close ribonucleotide residues in a query structure is compared to clusters of reference doublets obtained by analysis of a large number of experimentally determined RNA structures, and assigned a score that describes its similarity to one or more known types of contacts, including pairing, stacking, base–phosphate and base–ribose interactions.

      • BrickworX

        • BrickworX web server builds RNA and DNA models into electron density maps at resolutions as low as 4 Å. On input the program requires a MTZ file with structure factor amplitudes and phases. 

      • GDFuzz3D

        • GDFuzz3D is a method for protein 3D structure modeling, which starts from the protein sequence and a map of contacts between amino acid residues. It can handle predicted maps that contain e.g., probabilities of contacts between all residues, and a high fraction of incorrectly predicted contacts. It is not appropriate for predicting structures based on maps with only a few predicted contacts.

      • tRNAmodpred

        • The program takes as an input a set of unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell, identifies all RNA residues that correspond to known modification sites with known enzymes, finds homologs of known tRNA modification enzymes, and maps the predictions onto known pathways of RNA modification, to identify theoretically possible modification reactions for all positions in query tRNAs.

      • SupeRNAlign

        • SupeRNAlign is a tool for flexible superposition of RNA 3D structures. Our program implements an iterative algorithm that splits RNA structures into fragments and superimposes them using existing tools (currently R3D Align). Finally, the superimposed structures are saved to a .pdb file and a sequence alignment is generated.

    • TOOLKIT
  • Home
  • Funded grants
    • FNP (TEAM)

      • Modeling of dynamic interactions between RNA and small molecules and its practical applications (POIR.04.04.00-00-3CF0/16-00); 3 449 541 PLN; 2017-2020. PI: J.M.Bujnicki, vice-PI: F.Stefaniak

    • NCN (MAESTRO)

      • Integrative modeling and structure determination of macromolecular complexes comprising RNA and proteins (2017/26/A/NZ1/01083); 3 500 000 PLN; 2018-2023. PI: J.M.Bujnicki, vice-PI: N.Chandran

    • NCN (MINIATURA)

      • Photoswitchable ligands for riboswitches (2018/02/X/NZ1/01468); 21670 PLN 2018-2019. PI: F.Stefaniak

    • NCN (OPUS)

      • Development of new methods for designing RNA molecules that fold into desired spatial structures and their use for development of new functional RNAs and for prediction of noncoding RNAs in transcriptome sequences (2017/25/B/NZ2/01294); 1 494 250 PLN; 2018-2021. PI: J.M.Bujnicki, vice-PI: T.Wirecki

  • Achievements
  • Publications
  • In the media
  • People
  • Employment

Publications of the team

Members of the research groups in IIMCB (since 2001) and UAM (since 2004) are shown in colors

 

 

2019, and in press

 

  Jaciuk M, Swuec P, Gaur V, Kasprzak JM, Renault L, Dobrychłop M, Nirwal S, Bujnicki JM, Costa A, Nowotny M [pdf]

A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair

DNA Repair. 2020; January;85,102746
  Magnus M, Kappel K, Das R, Bujnicki JM [pdf]

RNA 3D structure prediction guided by independent folding of homologous sequences. 

BMC Bioinformatics. 2019 Oct 22;20(1):512.
  Radom M, Machnicka MA, Krwawicz J, Bujnicki JM, Formanowicz P [pdf]

Petri net-based model of the human DNA base excision repair pathway.

PLoS One. 2019 Sep 13;14(9):e0217913.
  Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM. [pdf]

Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com.

PLoS One. 2019 Apr 25;14(4):e0214481. 
  Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ.  [pdf]

Crystal structure and directed evolution of specificity of NlaIV restriction endonuclease.

J Mol Biol. 2019 Apr 14. pii: S0022-2836(19)30204-9. doi: 10.1016/j.jmb.2019.04.010.
  Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I.  [pdf]

Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.

Sci Rep. 2019 Apr 12;9(1):5965. doi: 10.1038/s41598-019-42435-z.
  Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM [pdf]

QRNAS: software tool for refinement of nucleic acid structures

BMC Struct Biol. 2019 Mar 21; 19(5); doi: 10.1186/s12900-019-0103-1
  de Crecy-Lagard V, Boccaletto P, Mangleburg C, Sharma P, Lowe T, Leidel S, Bujnicki JM  [pdf]

Matching tRNA modifications in humans to their known and predicted enzymes 

Nucleic Acids Res 2019 Mar 18; doi: 10.1093/nar/gkz011
  Ponce-Salvatierra A, Astha, Merdas K, Nithin C, Ghosh P, Mukherjee S, Bujnicki JM [pdf]

Computational modeling of RNA 3D structure based on experimental data

Biosci Rep. 2019 Feb 8;39(2).
  Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S [pdf]

RRMdb – an evolutionary-oriented database of RNA recognition motif sequences

Database 2019 Jan 1;2019. doi: 10.1093/database/bay148
  Sweeney BA, Petrov AI, Burkov B, Finn RD, Bateman A, Szymanski M, Karlowski WM, Gorodkin J, Seemann SE, Cannone JJ, Gutell RR, Fey P, Basu S, Kay S, Cochrane G, Billis K, Emmert D, Marygold SJ, Huntley RP, Lovering RC, Frankish A, Chan PP, Lowe TM, Bruford E, Seal R, Vandesompele J, Volders PJ, Paraskevopoulou M, Ma L, Zhang Z, Griffiths-Jones S, Bujnicki JM, Boccaletto P, Blake JA, Bult CJ, Chen R, Zhao Y, Wood V, Rutherford K, Rivas E, Cole J, Laulederkind SJF, Shimoyama M, Gillespie ME, Orlic-Milacic M, Kalvari I, Nawrocki E, Engel SR, Cherry JM, Team S, Berardini TZ, Hatzigeorgiou A, Karagkouni D, Howe K, Davis P, Dinger M, He S, Yoshihama M, Kenmochi N, Stadler PF, Williams KP. [pdf]

RNAcentral: a hub of information for non-coding RNA sequences

Nucleic Acids Res. 2019 Jan 8;47(D1):D1250-D1251


2018

 

  Toczydlowska-Socha D, Zielinska M, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM [pdf]

Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini

Philos Trans R Soc Lond B Biol Sci. 2018 Nov 5;373(1762). pii: 20180161. doi: 10.1098/rstb.2018.0161.
  Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU. [pdf]

The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity.

Nucleic Acids Res. 2018 Nov 2;46(19):10353-10367. doi: 10.1093/nar/gky668.
  Nithin C, Ghosh P, Bujnicki JM [pdf]

Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes

Genes (Basel). 2018 Aug 25;9(9). pii: E432. doi: 10.3390/genes9090432.
  Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M [pdf]

Crystal structure of human Acinus RNA recognition motif domain

PeerJ. 2018 Jul 4;6:e5163. doi: 10.7717/peerj.5163
  Kumari P, Aeschimann F, Gaidatzis D, Keusch J, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Grosshans H, Ciosk R  [pdf]

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition

Nat Commun. 2018 Apr 19;9(1):1549.
  Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.  [pdf]

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

RNA Biol. 2018 May 9:1-3.
  Foik IP, Tuszynska I, Feder M, Purta E, Stefaniak F, Bujnicki JM. [pdf]

Novel inhibitors of the rRNA ErmC' methyltransferase to block resistance to macrolides, lincosamides, streptogramine B antibiotics.

Eur J Med Chem. 2018 Feb 25;146:60-67. doi: 10.1016/j.ejmech.2017.
  Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki T, de Crécy-Lagard V, Ross R, Limbach P, Kotter A, Helm M, Bujnicki JM  [pdf]

MODOMICS: a database of RNA modification pathways. 2017 update

Nucleic Acids Res. 2018 Jan 4;46(D1):D303-D307. doi: 10.1093/nar/gkx1030 
  Boccaletto P, Magnus M, Almeida C, Zyla A, Astha, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki T, Boniecki M, Stefaniak F, Bujnicki JM [pdf]

RNArchitecture: a database and a classification system of RNA families, with a focus on structural information

Nucleic Acids Res. 2018 Jan 4;46(D1):D202-D205. doi: 10.1093/nar/gkx966 

 

2017
 

  Piatkowski P, Jablonska J, Zyla A, Niedzialek D, Matelska D, Jankowska E, Walen T, Dawson WK, Bujnicki JM. [pdf]

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.

Nucleic Acids Res. 2017 Sep 19;45(16):e150. doi: 10.1093/nar/gkx631.
  Dzananovic E, Astha, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA [pdf]

Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition

PLoS One. 2017 Oct 20;12(10):e0186849.
  Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L [pdf]

Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs

Nucleic Acids Res. 2017 Nov 2;45(19):11019-11032. doi: 10.1093/nar/gkx757 
  Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M [pdf]

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro

Sci Rep. 2017 Jun 20;7(1):3873. doi: 10.1038/s41598-017-03936-x 
  Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I [pdf]

Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates.

J Biol Chem. 2017 May 5;292(18):7507-7518. doi: 10.1074/jbc.M116.766709 
  Miao Z, Adamiak RW, Antczak M, Batey RT, Becka A, Biesiada M, Boniecki MJ, Bujnicki JM, Chen S, Cheng CY, Chou F, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B II, Xiao Y, Xu X, Zhang D, Zok T, Westhof E [pdf]

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116.
  Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell RR, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, SILVA team , Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders P, Mestdagh P, Wower J, Clark M, Quek XC, Dinger ME  [pdf]

RNAcentral: a comprehensive database of non-coding RNA sequences

Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134.

 

2016
 

  Patel T, Chojnowski G, Astha, Koul A, McKenna S, Bujnicki JM  [pdf]

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering and computational methods

Methods. 2016 Dec 8. doi: 10.1016/j.ymeth.2016.12.002 
  Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ [no pdf yet]

Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases

Sci Rep. 2016 Dec 7;6:38612
  Glow D, Nowacka M, Skowronek KJ, Bujnicki JM [pdf]

Sequence-specific endoribonucleases

Postepy Biochem. 2016, 62, 3:303 - 314
  Piatkowski P, Kasprzak JM, Kumar D, Magnus M, Chojnowski G, Bujnicki JM  [pdf]

RNA 3D structure modeling by combination of template-based method ModeRNA, template-free folding with SimRNA, and refinement with QRNAS

Methods Mol Biol. 2016;1490:217-35.
  Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN. [pdf]

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase.

Biochimie. 2016 Sep-Oct;128-129:70-82. doi: 10.1016/j.biochi.2016.07.006 
  Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM [pdf]

Coarse-grained modeling of RNA 3D structure

Methods 2016 Jul 1;103:138-56. doi: 10.1016/j.ymeth.2016.04.026.
  Madan B, Kasprzak JM, Tuszynska I, Magnus MM, Szczepaniak K, Dawson WK, Bujnicki JM [pdf]

Modeling of protein-RNA complex structures using computational docking methods

Methods Mol Biol. 2016;1414:353-72. doi: 10.1007/978-1-4939-3569-7_21.
  Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM [pdf]

SimRNAweb – a web server for RNA 3D structure modeling with optional restraints  

Nucleic Acids Res. 2016 Jul 8;44(W1):W315-9. doi: 10.1093/nar/gkw279.
  Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM [pdf]

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Methods. 2016 Sep 1;107:34-41. doi:10.1016/j.ymeth.2016.03.013 
  Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I [pdf]

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

DNA Res. 2016 Apr;23(2):135-43. doi: 10.1093/dnares/dsw003 
  Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S [pdf]

Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts

Genome Biol Evol. 2016 Jan 18;8(2):426-38. doi: 10.1093/gbe/evw007.
  Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, Valpuesta J  [pdf]

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex 

Nature Commun. 2016 7:10433 doi: 10.1038/ncomms10433
  Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM [pdf]

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

Nucleic Acids Res. 2016 Apr 20;44(7):e63, doi: 10.1093/nar/gkv1479 [Epub 2015 Dec 19]
  Dawson WK, Bujnicki JM [pdf]

Computational modeling of RNA 3D structures and interactions 

Curr Opin Struct Biol. 2016 Apr ;37:22-28. [Epub ahead of print 2015 Dec 12, doi: 10.1016/j.sbi.2015.11.007] 
  Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W [pdf]

Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue

Nucleic Acids Res 2016 Jan 29;44(2):940-53. doi: 10.1093/nar/gkv1369. [Epub 2015 Dec 15]

 

2015
 

  Machnicka AM, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM [pdf]

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes

BMC Bioinformatics 2015, 16:336  doi:10.1186/s12859-015-0773-z
  Plotka M, Kaczorowska AK, Morzywolek A, Makowska J, Kozlowski LP, Thorisdottir A, Skírnisdottir S, Hjörleifsdottir S, Fridjonsson OH, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T. [pdf]

Biochemical characterization and validation of a catalytic site of a highly thermostable Ts2631 endolysin from the Thermus scotoductus phage vB_Tsc2631. 

PLoS One. 2015 Sep 16;10(9):e0137374. doi: 10.1371/journal.pone.0137374.
  Stefaniak F, Chudyk E, Bodkin M, Dawson WK, Bujnicki JM  [pdf]

Modeling of RNA-ligand interactions

Wiley Interdiscip Rev Comput Mol Sci 2015 Sep 14, doi: 10.1002/wcms.1226 
  Czerwoniec A, Kasprzak JM, Bytner P, Dobrychlop M, Bujnicki JM [pdf]

Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome 

FEBS Lett 2015 Sep 14;589(19 Pt A):2603-10. doi:10.1016/j.febslet.2015.07.026. 
  Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC  [pdf]

A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing  

eLife 2015 Jul 10;4. doi: 10.7554/eLife.07320. 
   Pietal M, Bujnicki JM, Kozlowski LP  [pdf]

GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function 

Bioinformatics 2015 Nov 1;31(21):3499-505 [Epub ahead of print 2015 Jun 30. doi: 10.1093/bioinformatics/btv390]
  Chawla M, Oliva R, Bujnicki JM, Cavallo LBioinformatics 2015 Jun 30. pii: btv390. [Epub ahead of print]  [pdf]

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies 

Nucleic Acids Res. 2015 Aug 18;43(14):6714-29. doi: 10.1093/nar/gkv606. Epub 2015 Jun 27. 
  Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM [pdf]

NPDock – a web server for protein-nucleic acid docking 

Nucleic Acids Res 2015 Jul 1;43(W1):W425-30. doi: 10.1093/nar/gkv493. [Epub 2015 May 14]
  Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT  [pdf]

The signature of the five-stranded vRRM fold defined by functional, structural and computational analysis of the hnRNP L protein 

J Mol Biol. 2015 Sep 25;427(19):3001-22. doi: 10.1016/j.jmb.2015.05.020. 
  Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E  [pdf]

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

RNA. 2015 Jun;21(6):1066-84. 
  Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA [pdf]

Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-Oligoadenylate Synthetase family. 

J Struct Biol 2015 May;190(2):236-49. 
  Zheng H, Shabalin I, Handing K, Bujnicki JM, Minor M [pdf]

Magnesium binding architectures in RNA crystal structures: validation binding preferences, classification, and motif detection

Nucleic Acids Res 2015 Apr 20;43(7):3789-801. 
  Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM [pdf]

Brickworx builds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps

Acta Crystallogr D Biol Crystallogr 2015 Mar 1;71(Pt 3):697-705. [Epub 2015 Feb 26.] 
  Philips A, Lach G, Bujnicki JM [pdf]

Computational methods for prediction of RNA interactions with metal ions and small organic ligands 

Methods Enzymol 2015;553:261-85. doi: 10.1016/bs.mie.2014.10.057. [Epub 2015 Feb 3.]
  Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM [pdf]

Sequence-specific cleavage of dsRNA by Mini-III RNase

Nucleic Acids Res. 2015 Mar 11;43(5):2864-73. doi: 10.1093/nar/gkv009. [Epub 2015 Jan 29.] 
  RNAcentral Consortium (Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn R, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Cheng X, Bujnicki JM, Chua N, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang H, Huang H, Cherry JM, Pruitt KD)  [pdf]

RNAcentral: an international database of ncRNA sequences 

Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9. doi: 10.1093/nar/gku991 
 

Stefaniak F

 [pdf]
Prediction of Compounds Activity in Nuclear Receptor Signaling and Stress Pathway Assays Using Machine Learning Algorithms and Low-Dimensional Molecular Descriptors
Front. Environ. Sci. 2015 Dec 01, 3:77. doi: 10.3389/fenvs.2015.00077
 

Pyrka M, Maciejczyk M

 [pdf]
Theoretical study of tautomeric equilibria of 2,6-diamino-8-azapurineand 8-aza-iso-guanine
Chem Phys Letters 2015, 627, 30–35

 

2014
 

  Byszewska M, Smietanski M, Purta E, Bujnicki JM [pdf]

RNA methyltranserases involved in 5′ cap biosynthesis

RNA Biology 2014 Dec 2;11(12):1597-607. doi: 10.1080/15476286.2015.1004955.
  Machnicka M, Olchowik A, Grosjean H, Bujnicki JM [pdf]

Distribution and frequencies of post-transcriptional modifications in tRNAs 

RNA Biology 2014 Dec 2;11(12):1619-29. doi: 10.4161/15476286.2014.992273.  
  Nowis D, Malenda A, Furs K, Oleszczak B, Sadowski R, Chlebowska J, Firczuk M, Bujnicki JM, Staruch AD, Zagozdzon R, Glodkowska-Mrowka E, Szablewski L, Golab J  [pdf]

Statins impair glucose uptake in human cells

BMJ Open Diabetes Res Care. 2014 Apr 26;2(1):e000017. doi: 10.1136/bmjdrc-2014-000017. 
  Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S [pdf]

Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures

 J Struct Biol 2014 Nov;188(2):123-33. doi: 10.1016/j.jsb.2014.09.007 
  Grabowska AD, Wywiał E, Dunin-Horkawicz S, Lasica AM, Wösten MM, Nagy-Staroń A, Godlewska R, Bocian-Ostrzycka K, Pieńkowska K, Laniewski P, Bujnicki JM, van Putten JP, Jagusztyn-Krynicka EK  [pdf]

Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA

PLoS ONE. 2014 Sep 2;9(9):e106247. doi: 10.1371/journal.pone.0106247.
  Walen T, Chojnowski G, Gierski P, Bujnicki JM [pdf]

ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes

Nucleic Acids Res. 2014, doi: 10.1093/nar/gku76
  Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek KJ, Bujnicki JM, Dadlez M, Bochtler M [pdf]

Structural basis of the methylation specificity of R.DpnI.

Nucleic Acids Res. 2014 Sep 1;42(13):8745-54. doi: 10.1093/nar/gku546. Epub 2014 Jun 25. 
  Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Penafiel R  [pdf]

Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2 

FEBS OpenBio 2014 Jun 2;4:510-21. doi: 10.1016/j.fob.2014.05.004. eCollection 2014.
  Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z  [pdf]

Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production

BMC Plant Biol. 2014 Jun 17;14(1):168 
  Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM  [pdf]

Computational modeling of RNA 3D structures, with the aid of experimental restraints 

RNA Biol 2014 Apr 23;11(5). pii: 28826. Epub 2014 Apr 23. 
  Rother K, Rother M, Skiba P, Bujnicki JM [pdf]

Automated modeling of RNA 3D structure.

Methods Mol Biol. 2014;1097:395-415. doi: 10.1007/978-1-62703-709-9_18.
  Majorek K, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM [pdf]

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

Nucleic Acids Res 2014 Apr;42(7):4160-79. [Epub 2014, Jan 23, doi: 10.1093/nar/gkt1414] 
 

Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM

 [pdf]

Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation

Nature Commun 2014, 5:3004, doi:10.1038/ncomms4004
  Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K,Harding SE, Bujnicki JM, McKenna SA [pdf]

Solution conformation of Adenovirus Virus Associated RNA-I and its interaction with PKR

J Struct Biol 2014 Jan;185(1):48-57. doi: 10.1016/j.jsb.2013.11.007. [Epub 2013 Nov 28].
  Plotka M, Kaczorowska AK, Stefanska A, Morzywolek A, Fridjonsson O, Dunin-Horkawicz S, Kozlowski L, Hreggvidsson G, Kristjansson J, Dabrowski S, Bujnicki JM, Kaczorowski T [pdf]

Discovery and characterization of a novel highly thermostable endolysin from Thermus scotoductus MAT2119 bacteriophage Ph2119 that shows amino-acid sequence similarity to eukaryotic peptidoglycan recognition proteins (PGRPs)

Appl Env Microbiol 2014 Feb;80(3):886-95 [Epub 2013 Nov 22] 
  Chojnowski G, Walen T, Bujnicki JM [pdf]

RNA Bricks - a database of RNA 3D motifs and their interactions

Nucleic Acids Res 2014 Jan 1;42(1):D123-31. doi: 10.1093/nar/gkt1084. [Epub 2013 Nov 12 2013] 
  Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski L, Dunin-Horkawicz S, Bujnicki JM [pdf]

Computational modeling of protein-RNA complex structures

Methods. 2014 Feb;65(3):310-9. doi: 10.1016/j.ymeth.2013.09.014. Epub 2013 Sep 29. 

 

2013
 

  Philips A, Milanowska K, Lach G, Bujnicki JM [pdf]

LigandRNA: computational predictor of RNA-ligand interactions

RNA 2013 Dec;19(12):1605-16.
  Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S [pdf]

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

RNA 2013 Oct;19(10):1341-8.
  Pawlowski M, Bogdanowicz A, Bujnicki JM [pdf]

QA-RecombineIt: a server for quality assessment and recombination of protein models
Nucleic Acids Res 2013 Jul;41(Web Server issue):W389-97.
  Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J [pdf]
RNAlyzer – novel approach for quality analysis of RNA structural models
Nucleic Acids Res 2013 Jul;41(12):5978-90.
  Bujnicki JM, Tiuryn J [pdf]
Bioinformatics and computational biology in Poland
PLoS Comput Biol 2013 9(5): e1003048. doi:10.1371/journal.pcbi.1003048.
  Puton T, Kozlowski L, Rother KM, Bujnicki JM [pdf]
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction
Nucleic Acids Res 2013 Apr 1;41(7):4307-23. doi: 10.1093/nar/gkt101.
  Nowak E, Potrzebowski W, Konarev P, Rausch J, Bona M, Svergun D, Bujnicki JM, Le Grice S, Nowotny M [pdf]
Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid
Nucleic Acids Res 2013 Apr 1;41(6):3874-3887.
  Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM [pdf]
RNApathwaysDB – a database of RNA maturation and decay pathways
Nucleic Acids Res 2013 Jan 1;41(D1):D268-72 [Epub ahead of print 2012 Nov 15 doi:10.1093/nar/gks1052]
  Machnicka MA, Milanowska K, Osman Oglu O, Purta E, Kurkowska M, Olchowik A,Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H [pdf]
MODOMICS: a database of RNA modification pathways: 2012 update
Nucleic Acids Res 2013 Jan 1;41(D1): D262-D267 [Epub ahead of print 2012 Oct 30 doi:10.1093/nar/gks1007]
 

Pietal M

 [pdf]
Legal opportunities for software commercialization of Polish scientific units
PUG 2013 778(4):20-27
 

Ismer J, Rose AS, Tiemann JK, Goede A, Rother K, Hildebrand PW.

 [pdf]
Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.
Nucleic Acids Res. 2013 Jan 1;41(D1):D280-4. doi: 10.1093/nar/gks1061.

 

2012
 

  Pietal M, Szostak N, Rother KM, Bujnicki JM [pdf]
RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures
BMC Bioinformatics 2012 Dec 21;13(1):333.
  Pawlowski M, Bujnicki JM [pdf]
The utility of comparative models and their local quality for protein crystal structure determination by Molecular Replacement
BMC Bioinformatics 2012 Nov 5;13(1):289.
  Sulej A, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM [pdf]
Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger
Nucleic Acids Res 2012 Dec 1;40(22):11563-70.
  Korneta I, Bujnicki JM [pdf]
Intrinsic disorder in the human spliceosomal proteome
PLoS Comp Biol 2012 Aug;8(8):e1002641
  Magnus M, Pawlowski M, Bujnicki JM [pdf - proofs]
MetaLocGramN: a meta-predictor of protein subcellular localization for Gram-negative bacteria
Biochim Biophys Acta 2012, Dec;1824(12):1425-33
  Kasprzak JM, Czerwoniec A, Bujnicki JM [pdf preliminary]
Molecular evolution of dihydrouridine synthases
BMC Bioinformatics 2012 Jun 28;13(1):153
  Skowronek KJ, Boniecki M, Kluge B, Bujnicki JM [pdf]
Rational engineering of sequence specificity in R.MwoI restriction endonuclease
Nucleic Acids Res 2012 Sep 1;40(17):8579-92.
  Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM [pdf]
Delineation of structural domains and identification of functionally important residues in DNA repair enzyme Exonuclease VII
Nucleic Acids Res 2012 Sep 1;40(16):8163-74.
 

Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek KJ

 [pdf]
Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease R.DpnI
Nucleic Acids Res 2012 Aug 1;40(15):7563-72.
  Kozlowski LP, Bujnicki JM [pdf preliminary]
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins
BMC Bioinformatics 2012, May 24;13(1):111
 

Korneta I, Magnus M, Bujnicki JM

 [pdf]
Structural bioinformatics of the human spliceosomal proteome
Nucleic Acids Res 2012 Aug 1;40(15):7046-65.
 

Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, Bujnicki JM, Yahia S, Abdel-Hadi D, Hamed S, Puzianowska-Kuznicka M

 [pdf]
A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome
Eur J Human Genet 2012 Nov;20(11):1134-40
 

Malenda A, Skrobanska A, Issat T, Winiarska M, Bil J, Oleszczak B, Sinski M, Firczuk M, Bujnicki JM, Chlebowska J, Staruch AD, Glodkowska-Mrowka E, Kunikowska J, Krolicki L, Szablewski L, Gaciong Z, Koziak K, Jakobisiak M, Golab J, Nowis D

 [pdf]
Statins impair glucose uptake in tumor cells
Neoplasia 2012 Apr;14(4):311-23.
 

 Zylicz-Stachula A, Zolnierkiewicz O, Lubys A, Ramanauskaite D, Mitkaite G, Bujnicki JM, Skowron P

 [pdf]
Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities
BMC Mol Biol 2012 Apr 10;13(1):13
 

Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, SantaLucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E

 [pdf]
RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
RNA 2012 Apr;18(4):610-25. [Epub 2012 Feb 23]
 

Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versées W

 [pdf]
Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life
Nucleic  Acids Res 2012 Jun 1;40(11):5149-5161. [Epub ahead of print Feb 22]
 

Chojnowski G, Bujnicki JM, Bochtler M

 [pdf]
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes
Bioinformatics 2012 Mar 15;28(6):880-1. [Epub 2012 Jan 11]
 

Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versées W, Droogmans L

 [pdf]
The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA
RNA 2012 Apr;18(4):815-24. [Epub 2012 Feb 15]
 

Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H

 [pdf]
Crohn’s disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation
Mol Biol Evol 2012 Jun;29(6):1569-85. [Epub ahead of print Jan12]
 

Kennaway CK, Taylor JE, Song CF, Potrzebowski W, Nicholson W, White JH, Swiderska A, Obarska-Kosinska A, Callow P, Cooper LP, Roberts GA, Artero JB, Bujnicki JM, Trinick J, Kneale GG, Dryden DTF

 [pdf]
Structure and operation of the DNA-translocating Type I DNA restriction enzymes
Genes Dev 2012 Jan 1;26(1):92-104.
 

Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM

 [pdf]
MetalionRNA: computational predictor of metal-binding sites in RNA structures
Bioinformatics 2012 Jan 15;28(2):198-205. [Epub 2011 Nov 21]
 

Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM

 [pdf]
Computational methods for prediction of protein-RNA interactions
J Struct Biol 2012 Sep;179(3):261-8.
 

Rother K, Rother M, Boniecki M, Puton T, Tomala K, Lukasz P, Bujnicki JM

 [no pdf yet]
Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling
In "RNA Structure Prediction and Modelling". Editors: Leontis NB, Westhof E, Springer, 2012,  ISBN: 978-3-642-25739-1
 

Kozlowski L, Orlowski J, Bujnicki JM

 [no pdf yet]
Structure prediction of alternatively spliced proteins
In „Alternative pre-mRNA Splicing: Theory and Protocols: The Complete Guide for Biomedical Scientists”. Editors: Stamm S, Smith C, Luhrmann R, Wiley-Blackwell, 2012, ISBN: 978-3-527-32606-8
 

Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, Bujnicki JM

 [pdf]
A toolbox for developing bioinformatics software
Brief Bioinform 2012 Mar;13(2):244-57. [Epub 2011 Jul 29]
 

Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M 

 [pdf]
Novel nonspecific DNA adenine methyltransferases
Nucleic Acid Res 2012 Mar;40(5):2119-30.
 

Ramrath DJ, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, Loerke J, Scheerer P, Ivanov P, Teraoka Y, Shpanchenko O, Nierhaus KH, Spahn CM.

 [pdf]
The complex of tmRNA-SmpB and EF-G on translocating ribosomes.
Nature. 2012 May 6;485(7399):526-9. doi: 10.1038/nature11006.
 

Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.

 [pdf]
Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Brief Bioinform. 2012 May;13(3):383-9. doi: 10.1093/bib/bbr064
 

Lach G, DeKievet M, Jentschura UD

 [pdf]
Einstein–Hopf drag, Doppler shift of thermal radiation and blackbody drag: Three perspectives on quantum friction.
Cent Eur J Phys, 2012, 10(4), 763-767
 

Kusio-Kobialka M, Wolanin K, Podszywalow-Bartnicka P, Sikora E, Skowronek K, McKenna SL, Ghizzoni M, Dekker FJ, Piwocka K.

 [pdf]
Increased acetylation of lysine 317/320 of p53 caused by BCR-ABL protects from cytoplasmic translocation of p53 and mitochondria-dependent apoptosis in response to DNA damage.
Apoptosis. 2012 Sep;17(9):950-63. doi: 10.1007/s10495-012-0739-9.
 

Samluk L, Czeredys M, Skowronek K, Nałęcz KA

 [pdf]
Protein kinase C regulates amino acid transporter ATB(0,+).
Biochem Biophys Res Commun. 2012 May 25;422(1):64-9. doi: 10.1016/j.bbrc.2012.04.106.
 

Roszczenko P, Radomska KA, Wywial E, Collet JF, Jagusztyn-Krynicka EK.

 [pdf]
A novel insight into the oxidoreductase activity of Helicobacter pylori HP0231 protein.
PLoS One. 2012;7(10):e46563. doi: 10.1371/journal.pone.0046563.
 

Obrępalska-Stęplowska A, Budziszewska M, Wieczorek P, Czerwoniec A

 [pdf]
Analysis of two strains of Peanut stunt virus: satRNA-associated and satRNA free.
Virus Genes. 2012 Jun;44(3):513-21. doi: 10.1007/s11262-012-0729-6.


2011
 

 

Czerwoniec A, Bujnicki JM

 [pdf]
Identification and modeling of a phosphatase-like domain in a tRNA 2′-O-ribosyl phosphate transferase Rit1p
Cell Cycle 2011 Oct 15;10(20):3566-70
 

Bielska E, Lucas X, Czerwoniec A, Kasprzak JM, Kaminska KH, Bujnicki JM

 [pdf]
Virtual screening strategies in drug design - methods and applications
BioTechnnologia 2011, 92(3): 249-264
 

Rother M, Rother K, Puton T, Bujnicki JM

 [pdf]
RNA tertiary structure prediction with ModeRNA
Brief Bioinform 2011 Nov;12(6):601-13.
 

Tuszynska I, Bujnicki JM

 [pdf]
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
BMC Bioinformatics 2011 Aug 18;12(1):348
 

Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C

 [pdf]
RNAcentral: a vision for an international database of RNA sequences
RNA 2011 Nov;17(11):1941-6.
 

Liu J, Ganapathy K, Wywial E, Bujnicki JM, Nwogwugwu CA, Nes WD

 [pdf]
Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalyzed by Trypanosoma brucei sterol C24-methyltransferase
Biochem J 2011 Nov 1;439(3):413-22.
 

 Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM

 [pdf]
ModeRNA server: an online tool for modeling RNA 3D structures
Bioinformatics 2011 Sep 1;27(17):2441-2.
 

Milanowska K, Rother K, Bujnicki JM

 [pdf]
Databases and bioinformatics tools for the study of DNA repair
Mol Biol Int 2011, 475718. [Epub 2011 Jul 14] doi:10.4061/2011/475718
 

Sikorski K, Czerwoniec A, Bujnicki JM, Wesoly J, Bluyssen HAR

 [pdf]
STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease
Cytokine Growth Factor Rev 2011 Aug;22(4):211-9.
 

Spears JL, Rubio MA, Gaston KW, Wywial E, Strikoudis A, Bujnicki JM, Papavasiliou FN, Alfonzo JD

 [pdf]
A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase
J Biol Chem 2011 Jun 10;286(23):20366-74. [Epub 2011 Apr 20]
 

Mebrhatu M, Wywial E, Ghosh A, Michiels C, Lindner A, Taddei F, Bujnicki JM, van Melderen L, Aertsen A

 [pdf]
Evidence for an evolutionary antagonism between Mrr and Type III modification systems
Nucleic Acid Res 2011 Aug 1;39(14):5991-6001. [Epub 2011 Apr 19]
 

Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM

 [pdf]
2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family
Nucleic Acid Res 2011 Jun 1;39(11):4756-68. [Epub 2011 Feb 9]
 

Rother M, Rother K, Puton T, Bujnicki JM

 [pdf]
ModeRNA: A tool for comparative modeling of RNA 3D structure
Nucleic Acid Res 2011 May 1;39(10):4007-22. [Epub 2011 Feb 7]
 

Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM

 [pdf]

RNA and protein 3D structure modeling: similarities and differences

J Mol Model 2011 Sep;17(9):2325-36. [Epub 2011 Jan 22.]
 

Husain N, Obranić S, Koscinski L, Seetharaman J, Babić F, Bujnicki JM, Maravić-Vlahoviček G, Sivaraman J

 [pdf]
Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit
Nucleic Acids Res 2011 Mar 1;39(5):1903-1918. [Epub 2010 Nov 9]
 

 Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM

 [pdf]

REPAIRtoire – a database of DNA repair pathways

Nucleic Acids Res 2011 Jan;39(Database issue):D788-92. [Epub 2010 Nov 4]
 

Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun D, Taussig MJ

 [pdf proofs]
"4D Biology for Health and Disease" Workshop Report
New Biotechnol 2011 Jul;28(4):291-3. [Epub 2010 Oct 15]
 

Hasiów-Jaroszewska B, Czerwoniec A, Pospieszny H, Elena SF.

 [pdf]
Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein.
Virol J. 2011 Jun 24;8:318. doi: 10.1186/1743-422X-8-318.
 

Jaciuk M, Nowak E, Skowronek K, Tańska A, Nowotny M.

 [pdf]
Structure of UvrA nucleotide excision repair protein in complex with modified DNA.
Nat Struct Mol Biol. 2011 Feb;18(2):191-7.


2010
 

 

Gajda MJ, Tuszynska I, Kaczor M, Bakulina AY, Bujnicki JM

 [pdf]
FILTREST3D: discrimination of structural models using restraints from experimental data
Bioinformatics 2010 Dec 1;26(23):2986-7. [Epub 2010 Oct 17]
 

Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G

 [pdf]
Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair
Human Mut 2010 Aug;31(8):975-82.
 

Gajda MJ, Pawlowski M, Bujnicki JM

 [pdf proofs]
Protein structure prediction: from recognition of matches with known structures to recombination of fragments
In "Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies". Editor: Kolinski A, Springer, 2010, ISBN: 978-1-4419-6888-3
 

Kempenaers M, Roovers M, Oudjama Y, Tkaczuk KL, Bujnicki JM, Droogmans L

 [pdf]
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA
Nucleic Acids Res 2010 Oct 1;38(19):6533-43.
 

Chua TK, Seetharaman J, Kasprzak JM, Ng C, Patel BK, Love C, Bujnicki JM, Sivaraman J

 [pdf]
Crystal structure of a fructokinase homolog from Halothermothrix orenii
J Struct Biol 2010 Sep;171(3):397-401.
 

Pukszta S, Schilke B, Dutkiewicz R, Moczulska K, Stepien B, Kominek J, Reitenga KG, Bujnicki JM, Williams B, Craig EA, Marszalek J

 [pdf]
Co-evolution driven switch of J-protein specificity toward an Hsp70 partner
EMBO Rep 2010 May;11(5):360-5.
 

Husain N, Tkaczuk KL, Tulsidas SR, Kaminska KH, Čubrilo S, Maravić-Vlahoviček G, Bujnicki JM, Sivaraman J

 [pdf]
Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: A diversity of active sites in m7G methyltransferases
Nucleic Acids Res 2010 Jul 1;38(12):4120-32.
 

Zhang Z, Theler D, Kaminska KH, Hiller M, de la Grange P, Pudimat R, Rafalska I, Heinrich B, Bujnicki JM, Allain FHT, Stamm S

 [no pdf yet]
The YTH domain is a novel RNA binding domain
J Biol Chem 2010 May 7;285(19):14701-10.
 

Pukancsik M, Bekesi A, Klement Eva, Hunyadi-Gulyas E, Medzihradszky K, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vertessy B

 [pdf]
Physiological truncation and domain organization of a novel uracil-DNA degrading factor
FEBS J 2010 Mar;277(5):1245-59.
 

Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I

 [pdf]
A mobile genetic element of a novel type carrying a Type IIF restriction-modification system (PluTI)
Nucleic Acids Res 2010 May;38(9):3019-30
 

Zhou X, Khiang TC, Tkaczuk KL, Bujnicki JM, Sivaraman J

 [pdf]
Crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate binding pocket
J Struct Biol 2010 Mar;169(3):277-85.
 

Kaminska KH, Purta E, Hansen LH, Bujnicki JM, Vester B, Long KS

 [pdf]
Insights into the structure, function, and evolution of the Radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria
Nucleic Acids Res 2010 Mar 1;38(5):1652-63.
 

Tuszynska I, Bujnicki JM

 [pdf]
Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily
J Biomol Struct Dyn 2010; Feb;27(4):511-520.
 

Gille C, Bölling C, Hoppe A, Bulik S, Hoffmann S, Hübner K, Karlstädt A, Ganeshan R, König M, Rother K, Weidlich M, Behre J, Holzhütter HG.

 [pdf]
HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology.
Mol Syst Biol. 2010 Sep 7;6:411.
 

Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.

 [pdf]
BioCatalogue: a universal catalogue of web services for the life sciences.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W689-94.
 

Rother K, Rother M, Pleus A, Upmeier zu Belzen A.

 [pdf]
Multi-stage learning aids applied to hands-on software training.
Brief Bioinform. 2010 Nov;11(6):582-6.
 

Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Judge DP, van der Gool W, Brooksbank C.

 [pdf]
Bioinformatics training: a review of challenges, actions and support requirements.
Brief Bioinform. 2010 Nov;11(6):544-51. Epub 2010 Jun 18.
 

Rother K, Hoffmann S, Bulik S, Hoppe A, Gasteiger J, Holzhütter HG.

 [pdf]
IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities.
Biophys J. 2010 Jun 2;98(11):2478-86.


2009
 

 

Leski TA, Caswell CC, Pawlowski M, Klinke DJ, Bujnicki JM, Hart SJ, Lukomski S

 [pdf]
bcl genes of Bacillus cereus group organisms: Identification, classification and application in anthrax detection and fingerprinting
Appl Environ Microbiol 2009 Nov;75(22):7163-72. [Epub 2009 Sep 18.]
 

Kolmos E, Nowak M, Werner M, Fischer K, Schwarz G, Mathews S, Schoof H, Nagy F, Bujnicki JM, Davis SJ

 [pdf]
Integrating ELF4 into the circadian system through combined structural and functional studies
HFSP J 2009 Oct;3(5):350-366
 

Pena V, Jovin SM, Fabrizio P, Orlowski J, Bujnicki JM, Lührmann R, Wahl MC

 [pdf]
Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase
Mol Cell 2009 Aug 28;35(4):454-66
 

Palfi Z, Jae N, Preusser C, Kaminska KH, Bujnicki JM, Lee JH, Guenzl A, Kambach C, Urlaub H, Bindereif A

 [pdf]
SMN-assisted assembly of snRNP-specific Sm cores in Trypanosomes
Genes Dev 2009 Jul 15;23(14):1650-64.
 

Zylicz-Stachula A, Bujnicki JM, Skowron P

 [pdf]
Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family
BMC Mol Biol 2009 May 29;10(1):52.
 

Pawlowski M, Lasica A, Jagusztyn-Krynicka EK, Bujnicki JM

 [pdf]
AAN82231 protein from pathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family
Pol J Microbiol 2009;58(2):181-4
 

Purta E, O'Connor M, Bujnicki JM, Douthwaite S

 [pdf]
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA
Mol Microbiol 2009 Jun;72(5):1147-58. [Epub 2009 Apr 28]
 

Bauer RA, Rother K, Moor P, Reinert K, Steinke T, Bujnicki JM, Preissner R

 [pdf]
Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors
Algorithms 2009, 2(2), 692-709; doi:10.3390/a2020692
 

Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H

 [pdf]
Medaka: a promising model animal for comparative population genomics
BMC Res Notes 2009, May 10;2:88
 

Pierechod M, Nowak A, Saari A, Purta E, Bujnicki JM, Konieczny I

 [pdf proofs]
Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system
Protein Sci 2009 Mar;18(3):637-49.
 

Kennaway CK J, Obarska-Kosinska A, White JK, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J, Dryden DTF

 [pdf]
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
Nucleic Acids Res 2009 Feb;37(3):762-70. [Epub 2008 Dec 11.]
 

Nakonieczna J, Kaczorowski T, Obarska-Kosinska A, Bujnicki JM

 [pdf]
Functional analysis of the MmeI restriction-modification enzyme from a methanol utilizer Methylophilus methylotrophus: A subtype IIC enzyme related to Type I enzymes
Appl Environ Microbiol 2009 Jan;75(1):212-23. [Epub 2008 Nov 7]
 

Czerwoniec A, Kasprzak JM, Kaminska KH, Rother K, Purta E, Bujnicki JM

 [pdf]
Folds and functions of domains in RNA modification enzymes
In "DNA and RNA modification enzymes: comparative structure, mechanism, functions, cellular interactions and evolution". Editor: Grosjean H. Landes Bioscience 2009
 

Majorek K, Bujnicki JM

 [pdf]
Modeling of Escherichia coli Endonuclease V structure in complex with DNA
J Mol Model 2009 Feb;15(2):173-82. [Epub 2008 Nov 29]
 

Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak J, Bujnicki JM, Grosjean H, Rother K

 [pdf]
MODOMICS: a database of RNA modification pathways. 2008 update
Nucleic Acids Res 2009 Jan;37(Database issue):D118-21. [Epub 2008 Oct 14]
 

Cymerman IA, Rigden DJ, Bujnicki JM

 [no pdf available]
Prediction of protein function and features from theoretical models
In "From Protein Structure to Function with Bioinformatics". Editor: Rigden DJ. Springer 2009
 

Kocik E, Skowronek KJ, Kasprzak AA.

 [pdf]
Interactions between subunits in heterodimeric Ncd molecules.
J Biol Chem. 2009 Dec 18;284(51):35735-45.
 

Fink G, Hajdo L, Skowronek KJ, Reuther C, Kasprzak AA, Diez S.

 [pdf]
The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding.
Nat Cell Biol. 2009 Jun;11(6):717-23. Epub 2009 May 10.
 

Tkaczuk KL

 [pdf]
Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site.
J Mol Model. 2009 Aug 22. [Epub ahead of print]
 

Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R.

 [pdf]
Voronoia: analyzing packing in protein structures.
Nucleic Acids Res. 2009 Jan;37(Database issue):D393-5. Epub 2008 Oct 23.

 

2008
 

 

(editor) Bujnicki JM

  
Book: "Prediction of Protein Structures, Functions and Interactions". Wiley & Sons (2008), December 2008. 302 Pages, Hardcover.

ISBN-10: 0-470-51767-0, ISBN-13: 978-0-470-51767-3

 

Including 4 co-authored chapters:

 

 Kaminska KH, Milanowska K, Bujnicki JM

 [no pdf available]
The basics of protein sequence analysis
In "Prediction of Protein Structures, Functions and Interactions". Editor: Bujnicki JM. Wiley & Sons 2008
 

Majorek K, Kozlowski L, Jakalski M, Bujnicki JM

 [no pdf available]
First steps of protein structure prediction
In "Prediction of Protein Structures, Functions and Interactions". Editor: Bujnicki JM. Wiley & Sons 2008
 

Kosinski J, Tkaczuk KL, Kasprzak J, Bujnicki JM

 [no pdf available]
Template based prediction of three-dimensional protein structures: Fold recognition and comparative modeling
In "Prediction of Protein Structures, Functions and Interactions". Editor: Bujnicki JM. Wiley & Sons 2008
 

Tress, M, Gonzalo L, Bujnicki JM, Valencia A

 [no pdf available]
Integrating prediction of structures, functions, and interactions
In "Prediction of Protein Structures, Functions and Interactions". Editor: Bujnicki JM. Wiley & Sons 2008
 

Fukuda E, Kaminska KH, Bujnicki JM, Kobayashi I

 [pdf]
Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases
Genome Biol 2008 Nov 21;9(11):R163 [Epub ahead of print]
 

Orlowski J, Mebrhatu MT, Michiels CW, Bujnicki JM, Aertsen A

 [pdf]
Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr
Biochem Biophys Res Commun 2008 Dec 19;377(3):862-6. [Epub 2008 Oct 23]
 

Kaminska KH, Kawai M, Boniecki M, Kobayashi I, Bujnicki JM

 [pdf]
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site
BMC Struct Biol 2008 Nov 14;8(1):48.
 

Gyrd-Hansen M, Darding M, Miasari M, Santoro MM, Zender L, Xue W, Tenev T, da Fonseca PCA, Zvelebil M, Bujnicki JM, Lowe S, Silke J, Meier

 [pdf]

PIAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.
Nature Cell Biol 2008 Nov;10(11):1309-17. [Epub 2008 Oct 19]
 

Purta E, O'Connor M, Bujnicki JM, Douthwaite S

 [pdf]
YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962
J Mol Biol 2008 Nov 14;383(3):641-51. [Epub 2008 Aug 29]
 

Sunita S, Tkaczuk KL, Purta E, Kasprzak J, Douthwaite S, Bujnicki JM, Sivaraman J

 [pdf]
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes
J Mol Biol 2008 Nov 14;383(3):652-66. [Epub 2008 Aug 29]
 

Bauer RA, Rother K, Bujnicki JM, Preissner R

 [pdf]

Suffix techniques as a rapid method for RNA substructure search

Genome Inf 2008, 20:183-198
 

Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM

 [pdf]

MetaMQAP: a meta-server for the quality assessment of protein models

BMC Bioinformatics 2008 Sep 29;9(1):403
 

Purta E, Kaminska KH, Kasprzak J, Bujnicki JM, Douthwaite S

 [pdf]
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA
RNA 2008 Oct;14(10):2234-44. [Epub 2008 Aug 28]
 

Kosinski J, Plotz G, Guarne A, Bujnicki JM, Friedhoff P

 [pdf]
The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family
J Mol Biol 2008 Oct 10;382(3):610-27. [Epub 2008 Jun 28]
 

Khiang CT, Bujnicki JM, Chye TT, Huynh F, Patel BK, Sivaraman J

 [pdf]
Mechanism of action and binding mode revealed by the structure of sucrose phosphate synthase from Halothermothrix orenii
Plant Cell 2008 Apr;20(4):1059-72. [Epub Apr 18]
 

Orlowski J, Bujnicki JM

 [pdf]

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
Nucleic Acids Res 2008 Jun;36(11):3552-69. [Epub 2008 May 2]
 

Roovers M, Kaminska KH, Tkaczuk KL, Gigot D, Droogmans L, Bujnicki JM

 [pdf]

The YqfN protein of Bacillus subtilis is the tRNA:m1A22 methyltransferase (TrmK)
Nucleic Acids Res 2008 Jun;36(10):3252-62. [Epub 2008 Apr 17]
 

White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW

 [pdf]

Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits
Mol Cell Biol 2008 May;28(10):3151-61. [Epub 2008 Mar 10.]
 

Cymerman IA, Chung I, Beckmann BM, Bujnicki JM, Meiss G

 [pdf]
EXOG, a novel paralog of Endonuclease G in higher eukaryotes
Nucleic Acids Res 2008 Mar;36(4):1369-79. Epub 2008 Jan 10.
 

Mittra B, Zamudio JR, Bujnicki JM, Stepinski J, Darzynkiewicz E, Campbell DA, Sturm NR

 [pdf]
The TbMTr1 spliced leader RNA cap 1 2'-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity
J Biol Chem 2008 Feb 8;283(6):3161-72. [Epub 2007 Nov 29.]
 

Roovers M, Oudjama Y, Kaminska KH, Purta E, Caillet J, Droogmans L, Bujnicki JM

 [pdf]
Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the two last steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.
Proteins 2008 Jan 10;71(4):2076-2085
 

Feder M, Purta E, Koscinski L, Cubrilo S, Vlahovicek G, Bujnicki JM,

 [pdf]
Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics
ChemMedChem 2008 Feb 15;3(2):316-322.
 

Obarska-Kosinska A, Taylor JE, Callow P, Orlowski J, Bujnicki JM, Kneale GG

 [pdf]
HsdR subunit of the Type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling
J Mol Biol 2008 Feb 15;376(2):438-52. [Epub 2007 Nov 17]
 

Sen TZ, Kloster M, Jernigan RL, Kolinski A, Bujnicki JM, Kloczkowski A

 [pdf]
Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA
Biophys J 2008 Apr 1;94(7):2482-91. [Epub 2008 Jan 4]
 

Carpenter MA, Bujnicki JM, Bhagwat AS

 [pdf]
Is AID a monomer in solution?
DNA Repair 2008 Mar 1;7(3):349-50.
 

Kaminska KH, Bujnicki JM,

 [pdf proofs]
Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily
Cell Cycle 2008 Jan;7(1):120-1. [Epub 2007 Oct 11]
 

Vlahovicek-Maravic G, Cubrilo S, Tkaczuk KL, Bujnicki JM

 [pdf]
Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm
Biochim Biophys Acta 2008 Apr;1784(4):582-90. [Epub 2007 Sep 29]
 

Vasu K, Saravanan M, Bujnicki JM, Nagaraja V

 [pdf]
Structural integrity of the betabetaalpha-metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI
Biochim Biophys Acta 2008 Feb;1784(2):269-75.
 

Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM,

 [pdf]
Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA
Proteins 2008 Jan 1;70(1):1-18; [Epub 2007 Oct 1]
 

Godlewska R, Pawlowski M, Dzwonek A, Mikula M, Ostrowski J, Drela N, Jagusztyn-Krynicka EK.

 [pdf]
Tip-alpha (hp0596 gene product) is a highly immunogenic Helicobacter pylori protein involved in colonization of mouse gastric mucosa.
Curr Microbiol. 2008 Mar;56(3):279-86. Epub 2008 Jan 3
 

Smit S, Rother K, Heringa J, Knight R.

 [pdf]
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
RNA. 2008 Mar;14(3):410-6. Epub 2008 Jan 29.
 

Obrepalska-Steplowska A, Nowaczyk K, Budziszewska M, Czerwoniec A, Pospieszny H.

 [pdf]
The sequence and model structure analysis of three Polish peanut stunt virus strains.
Virus Genes. 2008 Feb;36(1):221-9. Epub 2007 Nov 30.

 

2007
 

 

Sabates-Bellver J, Van der Flier LG, de Palo M, Cattaneo E, Maake C, Rehrauer H, Laczko E, Kurowski MA, Bujnicki JM, Menigatti M, Luz J, Ranalli TV, Gomes V, Pastorelli A, Faggiani R, Anti M, Jiricny J, Clevers H, Marra G

 [pdf]

Transcriptome profile of human colorectal adenomas

Mol Cancer Res 2007 Dec;5(12):1263-75.
 

Ozanick SG, Bujnicki JM, Sem DS, Anderson JT

 [pdf]

Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding

Nucleic Acids Res 2007;35(20):6808-19. [Epub 2007 Oct 10]
 

Ibryashkina EM, Zakharova MV, Baskunov VB, Bogdanova ES, Nagornykh MO, Den'mukhamedov MM, Melnik BS, Kolinski A, Gront D, Feder M, Solonin AS, Bujnicki JM

 [pdf]
Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily
BMC Struct Biol 2007 Jul 12;7(1):48 [Epub ahead of print]
 

Liu Y, Li Z, Lin Q, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL

 [pdf]
Structure and evolutionary origin of Ca-dependent herring Type II antifreeze protein
PLoS ONE 2007 Jun 20;2:e548.
 

Zamudio JR, Mittra B, Foldynova-Trantirkova S, Zeiner GM, Luke J, Bujnicki JM, Sturm NR, Campbell DA

 [pdf proofs]

The 2'-O-ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei

Mol Cell Biol 2007 Sep;27(17):6084-92. [Epub 2007 Jul 2.]
 

Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A

 [pdf]
Identification of a single HNH active site in Type IIS restriction endonuclease Eco31I
J Mol Biol 2007 Jun 29;370(1):157-69. [Epub 2007 May 4]
 

Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J

 [pdf]
Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC
Nucleic Acids Res 2007 Jul 1;35(13):4264-4274. [Epub 2007 Jun 18]
 

Koscinski L, Feder M, Bujnicki JM,

 [pdf]
Identification of a missing sequence and functionally important residues of 16S rRNA:m1A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics
Cell Cycle 2007 May;6(10):1268-71. [Epub 2007 May 2]
 

Koudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Bujnicki JM, Gromova ES

 [pdf]
Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling
Mol Biol (Mosc.) 2007 41(5):806–19.
 

Pietal M, Tuszynska I, Bujnicki JM

 [pdf]
PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure
Bioinformatics 2007 Jun 1;23(11):1429-30. [Epub 2007 Mar 30]
 

Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM

 [pdf]
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
BMC Bioinformatics 2007, Mar 5;8:73. doi:10.1186/1471-2105-8-73
 

Kosinski J, Kubareva EA, Bujnicki JM

 [pdf]
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering
Proteins 2007 Jul 1;68(1):324-36. [Epub 2007 Apr 3]
 

Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I

 [pdf]
Novel protein fold discovered in the PabI family of restriction enzymes
Nucleic Acids Res 2007;35(6):1908-18. [Epub 2007 Mar 1]
 

Orlowski J, Boniecki M, Bujnicki JM

 [pdf]
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
Bioinformatics Mar 1;23(5):527-30. [Epub 2007 Jan 22]
 

Pena V, Liu S, Bujnicki JM, Luhrmann R, Wahl MC

 [pdf]
Structure of a multipartite protein-protein interaction domain in splicing factor Prp8 and its link to retinitis pigmentosa
Mol Cell 2007, Feb 23, 25, 615-624.
 

Skowronek KJ, Bujnicki JM

 [pdf]
Restriction and homing endonucleases.
In "Industrial Enzymes. Structure, Function and Applications"; Editors: Polaina J, MacCabe AP. Springer-Verlag 2007 ISBN: 978-1-4020-5376-4
 

Schafer P, Cymerman IA, Bujnicki JM, Meiss G

 [pdf]
Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: Evidence for a pseudodimeric structure of the active enzyme species
Protein Sci 2007 Jan;16(1):82-91.
 

Chovancova E, Kosinski J, Bujnicki JM, Damborsky J

 [pdf]
Phylogenetic analysis of haloalkane dehalogenases
Proteins 2007 May 1;67(2):305-16.
 

Sasin JM, Godzik A, Bujnicki JM

 [pdf]
SURF'S UP! - protein classification by surface comparisons
J Biosci 2007 Jan;32(1):97-100.
 

Hodis E, Schreiber G, Rother K, Sussman JL.

 [pdf]
eMovie: a storyboard-based tool for making molecular movies.
Trends Biochem Sci. 2007 May;32(5):199-204. Epub 2007 Apr 19.

2006
 

 

Wyszynska A, Pawlowski M, Bujnicki JM, Pawelec D, Van Putten JP, Brzuszkiewicz E, Jagusztyn-Krynicka EK

 [no pdf available]
Genetic characterisation of the cjaAB operon of Campylobacter coli
Pol J Microbiol 2006;55(2):85-94.
 

Gros L, Renodon-Corniere A, de Saint Vincent BR, Feder M, Bujnicki JM, Jacquemin-Sablon A

 [pdf]
Characterization of PRMT7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors
Biochim Biophys Acta 2006 Nov;1760(11):1646-56. Epub 2006 Sep 14.
 

Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM

 [pdf]
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase
BMC Mol Biol 2006 Jul 18;7:23
 

Carpenter M, Divvela P, Pingoud V, Bujnicki JM, Bhagwat AS.

 [pdf]
Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI
Nucleic Acids Res 2006 Aug 7;34(13):3770-8.
 

Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM.

 [pdf]
Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease.
Proteins 2006 Dec 1;65(4):867-76. [Epub Oct 6]
 

Han R, Lukomska E, Caswell CC, Keene DR, Pawlowski M, Bujnicki JM, Lukomski S

 [pdf]
Binding of the low density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes
Mol Microbiol 2006 Jul;61(2):351-67.
 

Dunin-Horkawicz S, Feder M, Bujnicki JM

 [pdf]
Phylogenomic analysis of the GIY-YIG nuclease superfamily
BMC Genomics 2006 Apr 28;7(1):98
 

Zamudio JR, Mittra B, Zeiner GM, Feder M, Bujnicki JM, Sturm NR, Campbell DA

 [pdf]
Complete cap 4 formation is not required for viability in Trypanosoma brucei
Eukaryotic Cell 2006 Jun;5(6):905-15.
 

Gabant G, Auxilien S, Tuszynska I, Locard M, Gajda MJ, Chaussinand G, Fernandez B, Dedieu1 A, Grosjean H, Golinelli-Pimpaneau B, Bujnicki JM, Armengaud J.

 [pdf]
THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.
Nucleic Acids Res 2006 May 10;34(9):2483-94.
 

Obarska A, Blundell A, Feder M, Patel J, Vejsadova S, Sisakova E, Weiserova M, Bujnicki JM, Firman K.

 [pdf]
Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.
Nucleic Acids Res 2006 Apr 13;34(7):1992-2005.
 

Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L.

 [pdf]
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
Nucleic Acids Res 2006 Apr 5;34(6):1925-34.
 

Sikora E, Bielak-Zmijewska A, Magalska A, Piwocka K, Mosieniak G, Kalinowska M, Widlak P, Cymerman IA, Bujnicki JM.

 [pdf]
Curcumin induces caspase-3 dependent apoptotic pathway but inhibits DFF40/CAD endonuclease in human Jurkat cells.
Mol Cancer Ther 2006 Apr;5(4):927-34.
 

Tkaczuk KL, Obarska A, Bujnicki JM.

 [pdf]
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.
BMC Evol Biol 2006 Jan 24;6(1):6
 

Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN.

 [pdf]
Functional analysis of amino acid residues in the dimerisation interface of KpnI DNA methyltransferase.
Biol Chem 2006 May;387(5):515-23.
 

Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS.

 [pdf]
Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair.
Chem Rev 2006 Feb;106(2):700-19.
 

Chiang PK, Bujnicki JM, Su XZ, Lanar DE.

 [pdf]
Malaria: therapy, genes and vaccines.
Current Mol Med 2006 May; 6(3):309-26
 

Skowronek KJ, Kosinski J, Bujnicki JM.

 [pdf]
A theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold-recognition and validated by site-directed mutagenesis.
Proteins 2006 Jun 1;63(4):1059-68.
 

Mikula M, Karczmarski J, Dzwonek A, Rubel T, Hennig E, Dadlez M, Bujnicki JM, Bomsztyk K, Ostrowski J

 [pdf]
Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length.
Biochim Biophys Acta 2006 Feb;1764(2):299-306.
 

Klimek-Tomczak K, Mikula M, Dzwonek A, Paziewska A, Karczmarski J, Hennig E, Bujnicki JM, Bragoszewski P, Denisenko O, Bomsztyk K, Ostrowski J.

 [pdf]
Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.
Br J Cancer 2006 Feb 27;94(4):586-92.
 

Metz J, Wachter A, Schmidt B, Bujnicki JM, Schwappach B.

 [pdf]
The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol.
J Biol Chem 2006 Jan 6;281(1):410-7. Epub 2005 Oct 31.
 

Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM

 [pdf]
MODOMICS: a database of RNA modification pathways.
Nucleic Acids Res 2006 Jan 1;34(Database issue):D145-9
 

Bujnicki JM

 [pdf]
Protein structure prediction by recombination of fragments
ChemBioChem 2006 Jan 9;7(1):19-27.
 

Godlewska R, Dzwonek A, Mikula M, Ostrowski J, Pawlowski M, Bujnicki JM, Jagusztyn-Krynicka EK,

 [pdf]
Helicobacter pylori protein oxidation influences the colonization process.
Inter J Med Microbiol 2006 Aug;296(4-5):321-4.

 

2005
 

 

Smiech B, Kazmierkiewicz R, Bujnicki JM, Lammek B

 [pdf]
Theoretical predictions of the impact of the trisubstituted pyrophosphate internucleotide bond on B DNA fragments
J Mol Struct THEOCHEM 2005 756: 63–71
 

Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosinski J, Lubys A.

 [pdf]
Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.
J Biol Chem 2005 Dec 16;280(50):41584-94. Epub 2005 Oct 11.
 

Cymerman IA, Meiss G, Bujnicki JM

 [pdf]
DNase II is a member of the phospholipase D superfamily.
Bioinformatics 2005 Nov 1;21(21):3959-62
 

Kosinski J, Feder M, Bujnicki JM

 [pdf]
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function
BMC Bioinformatics 2005 Jul 12;6(1):172
 

Ishikawa K, Watanabe M, Kuroita T, Uchiyama I, Bujnicki JM, Kawakami B, Tanokura M, Kobayashi I

 [pdf]
Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi
Nucleic Acids Res 2005 Jul 21;33(13):e112
 

Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P

 [pdf]
Analysis of the quaternary structure of the MutL C-terminal domain
J Mol Biol 2005 Aug 26;351(4):895-909.
 

Radlinska M, Piekarowicz A, Galimand M, Bujnicki JM

 [pdf]
Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by a transposon Tn1549 from Enterococcus spp.
Pol J Microbiol 2005 54(3), 249-252
 

Tkaczuk KL, Bujnicki JM, Bialkowska A, Bielecki S, Turkiewicz M, Cieslinski H, Kur J

 [pdf]
Molecular modelling of a psychrophilic beta-galactosidase
Biocatal Biotransform 2005 23(3/4), 201-209
 

Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M

 [pdf]
FRankenstein becomes a cyborg: the automatic recombination and realignment of Fold-Recognition models in CASP6
Proteins 2005;61 Suppl 7:106-13.
 

Kolinski A, Bujnicki JM

 [pdf]
Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models
Proteins 2005;61 Suppl 7:84-90.
 

Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud AM

 [pdf]
Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII
Mol BioSyst 2005 1(2):135-141. DOI: 10.1039/b503091a
 

Purushothaman SK, Grosjean H, Bujnicki JM, Lapeyre B

 [pdf]
Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA
Mol Cell Biol 2005 Jun;25(11):4359-70
 

Chmiel AA, Radlinska M, Pawlak SD, Krowarsch D, Bujnicki JM, Skowronek KJ 

 [pdf]
A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold-recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy
Protein Eng Des Sel 2005 Apr;18(4):181-189
 

Pawlak SD, Radlinska M, Chmiel AA, Bujnicki JM, Skowronek KJ

 [pdf]
Inference of relationships in the "twilight zone" of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII
Nucleic Acids Res 2005 Jan 31;33(2):661-71.
 

Feder M, Bujnicki JM

 [pdf]
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site
BMC Genomics 2005 Feb 18;6(1):21
 

Chmiel AA, Bujnicki JM, Skowronek KJ

 [pdf]
A homology model of restriction endonuclease SfiI in complex with DNA
BMC Struct Biol 2005 Jan 24;5(1):2.
 

Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek KJ, Droogmans L, Bujnicki JM

 [pdf]
Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis
Proteins 2005 May 15;59(3):482-8.
 

Raczko A, Bujnicki JM, Pawlowski M, Godlewska R, Lewandowska M, Jagusztyn-Krynicka EK

 [pdf]
Characterisation of new DsbB-like thiol-oxidoreductases of Campylobacter jejuni and Helicobacter pylori and classification of the DsbB family based on phylogenomic, structural, and functional criteria
Microbiology 2005 Jan;151(Pt 1):219-31.
 

Radlinska M, Kondrzycka-Dada A, Piekarowicz A, Bujnicki JM

 [pdf]
Identification of amino acids important for the target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.
Proteins 2005 Feb 1;58(2):263-70.
 

Pingoud V, Sudina A, Geyer H, Bujnicki JM, Lurz R, Luder G, Morgan R, Kubareva E, Pingoud A

 [pdf]
Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences
J Biol Chem 2005 Feb 11;280(6):4289-98. Epub 2004 Nov 24.

 

2004
 

 

Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V

 [pdf]

Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily

Nucleic Acids Res 2004 Nov 23;32(20):6129-6135
 

Ye X, O'Neil PK, Foster AN, Gajda MJ, Kosinski J, Kurowski MA, Bujnicki JM, Friedman AM, Bailey-Kellogg C

 [pdf]
Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure
Protein Sci 2004 Dec;13(12):3298-313
 

Paziewska A, Wyrwicz LS, Bujnicki JM, Bomsztyk K, Ostrowski J

 [pdf]
Cooperative binding of the hnRNP K three KH domains to mRNA targets
FEBS Lett 2004 Nov 5;577(1-2):134-40.
 

Koudan EV, Bujnicki JM, Gromova ES

 [pdf]
Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.
J Biomol Struct & Dyn 2004 Dec;22(3):339-46.
 

Armengaud J, Urbonavicius J, Fernandez B, Chaussinand G, Bujnicki JM, Grosjean H

 [pdf]
N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain containing, AdoMet-dependent methyltransferase, conserved in Archaea and Eukaryota
J Biol Chem 2004 Aug 27;279(35):37142-52
 

Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L

 [pdf]
Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA
RNA 2004 Aug;10(8):1236-42.
 

Sasin JM, Bujnicki JM

 [pdf]
COLORADO3D, a web server for the visual analysis of protein structures
Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W586-9.
 

Bujnicki JM, Feder M, Ayres CL, Redman KL

 [pdf]
Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases
Nucleic Acids Res 2004 Apr 30;32(8):2453-63.
 

Schafer P, Scholz SR, Gimadutdinow O, Cymerman IA, Bujnicki JM, Ruiz-Carrillo A, Pingoud A, Meiss G.

 [pdf]
Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis.
J Mol Biol 2004 Apr 23;338(2):217-28.
 

Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L.

 [pdf]
A primordial RNA modification enzyme: the case of tRNA:m1A methyltransferase
Nucleic Acids Res 2004 Jan 22; 32(2):465-476
 

Nes WD, Jayasimha P, Zhou W, Kanagasabai R, Jin C, Jaradat TT, Shaw RW, Bujnicki JM 

 [pdf]
Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis.
Biochemistry 2004 Jan 20;43(2):569-76.
 

Potluri S, Khan AA, Kuzminykh A, Bujnicki JM, Friedman AM, Bailey-Kellogg C

 [pdf]
Geometric analysis of cross-linkability for protein fold discrimination
Pac Symp Biocomput 2004 447-58
 

Bujnicki JM

 [pdf]
Molecular phylogenetics of restriction endonucleases.
In "Restriction Endonucleases: Structure, Function, and Evolution", Vol. 14 in Nucleic Acids and Molecular Biology series; Editor: Pingoud AM. Springer-Verlag 2004

 

Book: "Practical Bioinformatics". Vol. 15 in Nucleic Acids and Molecular Biology series; Editor: Bujnicki JM, Springer-Verlag 2004; ISBN: 3-540-20613-2
including 3 chapters:

 

 

Cymerman IA, Feder M, Pawlowski M, Kurowski MA, Bujnicki JM

 [pdf]
Computational methods for protein structure prediction and fold-recognition.
In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag 2004
 

Bujnicki JM, Fischer D

 [pdf]
'Meta' approaches to protein structure prediction.
In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag 2004
 

Bujnicki JM, Droogmans L, Grosjean H, Purushothaman SK, Lapeyre B

 [pdf]
Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases.
In Nucleic Acids and Molecular Biology series, "Practical Bioinformatics". Editor: Bujnicki JM. Springer-Verlag 2004
 

Maravic G, Bujnicki JM, Flogel M.

 [pdf]
Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'
Folia Microbiol 2004;49(1):3-7.
 

Rychlewski L, Bujnicki JM, Fischer D

 [pdf]
Protein fold-recognition and experimental structure determination.
In "The New Avenues in Bioinformatics", Vol 8 in the COLE series, "Origins: genesis, evolution and diversity of life". Editor: Seckbach J, Rubin E. Springer-Verlag 2004, ISBN 1-4020-2639-0

 

2003
 

 

Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM 

 [pdf]
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.
BMC Genomics 2003 4:48
 

Bujnicki JM

 [pdf]
Crystallographic and bioinformatics studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology.
Current Protein and Peptide Science 2003 Oct;4(5):327-37.
 

Scholz SR, Korn C, Bujnicki JM, Gimadutdinow O, Pingoud A, Meiss G.

 [pdf]
Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.
Biochemistry 2003 Aug 12;42(31):9288-94.
 

Maravic G, Bujnicki JM, Feder M, Pongor S, Flogel M.

 [pdf]
Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model of protein-RNA interactions
Nucleic Acids Res 2003 Aug 15;31(16):4941-9.
 

Maravic G, Feder M, Pongor S, Flogel M, Bujnicki JM.

 [pdf]
Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'
J Mol Biol 2003 Sep 5;332(1):99-109.
 

Gordon R, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie M, Hershfield MS, Bujnicki JM, Chiang PK.

 [pdf]
Anti-HIV-1 activity of 3-deaza-adenosine analogs: inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners
Eur J Biochem 2003 Sep;270(17):3507-3517.
 

Mouaikel J, Bujnicki JM, Tazi J, Bordonne R.

 [pdf]
Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA hypermethylase
Nucleic Acids Res 2003 Aug 15;31(16):4899-909
 

Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM

 [pdf]
A 'Frankenstein's monster' approach to comparative modeling: merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation.
Proteins 2003 53 Suppl 6:369-79. (CASP5 special issue)
 

Kurowski MA, Bujnicki JM 

 [pdf]
GeneSilico protein structure prediction meta-server
Nucleic Acids Res 2003 Jul 1;31(13):3305-7.
 

Ginalski K, Pas J, Wyrwicz LS, von Grotthuss M, Bujnicki JM, Rychlewski L

 [pdf]
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
Nucleic Acids Res 2003 Jul 1;31(13):3804-7.
 

Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM 

 [pdf]
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.
BMC Bioinformatics 2003 Mar 14;4(1):9.
 

Sasin JM, Kurowski MA, Bujnicki JM

 [pdf]
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification
Bioinformatics 2003 Jul;19 Suppl 1:I252-I254
 

Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Luder G, Xu S-Y, Pingoud AM

 [pdf]
PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes
J Mol Biol 2003 Jun 20;329(5):913-29.
 

Bujnicki JM, Albert MA, Nelson DJ, Thurlow DL

 [pdf]
Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii.
Proteins 2003 Aug 15;52(3):349-59.
 

Bujnicki JM, Prigge TS, Caridha D, Chiang PK

 [pdf]
Structure, evolution, and inhibitor interaction of S-Adenosyl-L-homocysteine hydrolase from Plasmodium falciparum
Proteins 2003 Sep 1;52(4):624-32.
 

Tchernaenko V, Radlinska M, Drabik C, Bujnicki JM, Halvorson HR, Lutter LC

 [pdf]
Topological measurement of an A-tract bend angle: I. Comparison of the bent and straight states
J Mol Biol 2003 Feb 21;326(3):737-49.
 

Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H

 [pdf]
Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures.
Nucleic Acids Res 2003 Apr 15;31(8):2148-56
 

De Bie LGS, Roovers M, Oudjama Y, Wattiez R, Tricot C, Stalon V, Droogmans L, Bujnicki JM

 [pdf]
The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase.
J Bacteriol 2003 May;185(10):3238-43.
 

Feder M, Pas J, Wyrwicz SL, Bujnicki JM

 [pdf]
Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases.
Gene 2003 Jan 2;302(1-2):129-38.

 

2002
 

 

Bujnicki JM, Feder M, Rychlewski L, Fischer D,

 [pdf]
Errors in the D. radiodurans large ribosomal subunit structure detected by fold recognition and structure evaluation tools
FEBS Lett 2002 Aug 14;525(1-3):174.
 

Godlewska R, Bujnicki JM, Ostrowski J, Jagusztyn-Krynicka EK

 [pdf]
The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor.
FEBS Lett 2002 Aug 14;525(1-3):39.
  Bujnicki JM, Feder M, Radlinska M, Blumenthal RM. [pdf]
Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m6A methyltransferase
J Mol Evol 2002 Oct;55(4):431-44.
 

Bujnicki JM, Rychlewski L

 [pdf]
In silico identification, structure prediction, and phylogenetic analysis of the 2'-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA negative-strand viruses.
Protein Eng 2002 Feb;15(2):101-8.
 

Pintard L, Lecointe F, Bujnicki JM, Bonnerot C, Grosjean H, Lapeyre B

 [pdf]
Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop
EMBO J 2002 Apr 2;21(7):1811-20.
 

Pingoud V, Kubareva E, Stengel G, Friedhoff P, Bujnicki JM, Urbanke C, Sudina A, Pingoud A

 [pdf]
Evolutionary relationship between different subgroups of restriction endonucleases
J Biol Chem 2002 Apr 19;277(16):14306-14.
 

Xu Y, Keene DR, Bujnicki JM, Hook M, Lukomski S

 [pdf]
Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices
J Biol Chem 2002 Jul 26;277(30):27312-8
 

Bujnicki JM, Blumenthal RM, Rychlewski L.

 [pdf]
Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus.
J Mol Microbiol Biotechnol 2002 Jan;4(1):93-9.
 

Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C

 [pdf]
MRM2 encodes a novel mitochondrial 21S rRNA methyltransferase
EMBO J. 2002 Mar 1;21(5):1139-1147.
 

Bujnicki JM, Rychlewski L

 [pdf]
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
BMC Bioinformatics 2002 Apr 3;3(1):10.
 

Bujnicki JM, Rychlewski L

 [pdf]
Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases
DNA Repair 2002 34:1-5
 

Bujnicki JM, Rychlewski L, Fischer D,

 [pdf]
Fold-recognition detects an error in Protein Data Bank
Bioinformatics 2002 18(10):1391-1395.
 

Bujnicki JM,

 [pdf]
Sequence permutations in the molecular evolution of DNA methyltransferases
BMC Evol Biol 2002 Mar 12;2(1):3
 

Bujnicki JM, Leach RA, Debski J, Rychlewski L

 [pdf]
Bioinformatic analysis of the tRNA:(guanine 26, N2,N2)-dimethyltransferase (Trm1) family.
J Mol Microbiol Biotechnol 2002 4(4):405-15.
 

Zhang P, Nicholson DE, Bujnicki JM, Su X, Brendle JJ, Ferdig M, Kyle DE, Milhous WK, Chiang PK

 [pdf]
Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis.
J Biomed Sci. 2002 9(1):34-40
 

Lutter LC, Tchernaenko V, Radlinska M, Drabik CE, Bujnicki JM, Halvorson HR

 [pdf - not available]
Measurement of DNA bend angles using DNA topology.
In "New Approaches to Structural Mechanics, Shells and Biological Structures" (Drew HR & Pellegrino S, eds), pp. 475-484, Kluwer, Dordrecht. 2002

 

2001
 

 

Bujnicki JM, Radlinska M, Rychlewski L

 [pdf]
Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed.
Trends Biochem Sci 2001 26(1):9-11
 

Bujnicki JM 

 [pdf]
In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea
FEBS Lett 2001 507(2): 123-127)
 

Bujnicki JM, Rychlewski L

 [pdf]
Identification of a PD-(D/E)XK-like domain with a novel configuration of the endonuclease active site in the methyl-directed restriction enzyme Mrr and its homologs from all three domains of life.
Gene 2001 267(2):183-91
 

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

 [pdf]
LiveBench-2: Large-scale automated evaluation of protein structure prediction servers
Proteins 2001; Suppl 5:184-91.
 

Bujnicki JM, Elofsson A , Fischer D, Rychlewski L

 [pdf]
Structure Prediction Meta Server.
Bioinformatics 2001 17(8):750-751.
 

Bujnicki JM

 [pdf]
Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.
Acta Biochim Pol 2001 48(4), 935-967
 

Bujnicki JM, Radlinska M, Zaleski P, Piekarowicz A

 [pdf]
Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage.
Acta Biochim Pol 2001 48(4), 969-983
 

Bujnicki JM

 [pdf]
A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide
Acta Microbiol Pol 2001 50, 219-229
 

Bujnicki JM, Rychlewski L

 [pdf]
Unusual evolutionary history of the tRNA splicing endonuclease EndA: Relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases
Protein Sci 2001 10: 656-660
 

Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L

 [pdf]
Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics
Protein Eng 2001 14(10):717-721.
 

Lundstrom J, Rychlewski L, Bujnicki JM, Elofsson A

 [pdf]
Pcons: a neural network based consensus predictor that improves fold recognition.
Protein Sci 2001 10(11):2354-62.
 

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

 [pdf]
LiveBench-1: continuous benchmarking of protein structure prediction servers.
Protein Sci 2001 10: 352-361
 

Radlinska M, Bujnicki JM

 [pdf]
Cloning of enterohemorrhagic Escherichia coli phage VT-2 Dam methyltransferase.
Acta Microbiol Pol 2001 50(2), 157-163
 

Bujnicki JM, Rychlewski L

 [pdf]
Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases.
Acta Microbiol Pol 2001 50(1), 7-17
 

Bujnicki JM, Rychlewski L

 [pdf]
The Herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis.
Virus Genes 2001 22(2):219-230
 

Radlinska M, Bujnicki JM

 [pdf]
Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA:m4C methyltransferase M.NgoMXV
Acta Microbiol Pol 2001 50(2), 93-101
 

Bujnicki JM, Rychlewski L

 [pdf]
Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles.
J Mol Microbiol Biotechnol 2001 3(1):69-72
 

Bujnicki JM, Rychlewski L

 [pdf]
Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda2 protein 
Genome Biology 2001 2(9):38
 

Bujnicki JM, Radlinska M.

 [pdf]
Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV.
Acta Microbiol Pol 2001 50(2), 151-166
 

Bujnicki JM, Feder M, Radlinska M, Rychlewski L

 [pdf]
mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.
BMC Bioinformatics 2001 2:2

 

2000
 

 

Bujnicki JM 

 [pdf]
Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and domain structure similar to other nucleic acid amino-methyltransferases
FASEB J 2000 14(14):2365-2368
 

Bujnicki JM

 [pdf]
Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.
J Mol Evol 2000 50(1):39-44
 

Bujnicki JM, Radlinska M, Rychlewski L

 [pdf]
Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc-finger and structural similarity to beta-beta-alpha-Me endonucleases
Mol Microbiol 2000 37(5):1280-1281
 

Bujnicki JM

 [pdf]
Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases
Acta Microbiol Pol 2000 49(1):19-29
 

Bujnicki JM, Rychlewski L

 [pdf]
Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease - implications for the evolution of the EndA/Sen family.
FEBS Lett 2000 486(3):328-329
 

Bujnicki JM, Rychlewski L

 [pdf]
Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs
Acta Microbiol Pol 2000 49(3-4):253-261
 

Bujnicki JM 

 [pdf]
Homology modelling of the DNA m5C methyltransferase M.BssHII. Is permutation of functional subdomains common to all subfamilies of DNA methyltransferases?
Int J Biol Macromol 2000 27(3):195-204

 

1999
 

 

Bujnicki JM, Radlinska, M

 [pdf]
Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin.
Nucleic Acids Res 1999 27(22):4501-4509
 

Bujnicki JM, Radlinska, M

 [pdf]
Is the HemK family of putative S-adenosylmethionine dependent methyltransferases a missing zeta subfamily of adenine methyltransferases? A hypothesis.
IUBMB Life 1999 48(3):247-249
 

Bujnicki JM

 [pdf]
Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation.
In Silico Biol 1: 1-8 (1999)
 

Bujnicki JM, Radlinska, M

 [pdf]
Molecular phylogenetics of DNA 5mC-methyltransferases.
Acta Microbiol Pol,1999 48(1):19-30
 

Radlinska, M., Bujnicki JM, Piekarowicz, A

 [pdf]
Structural characterization of two tandemly arranged DNA methyltransferases genes from Neisseria gonorrhoeae MS11: N-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
Proteins 1999 37(4):717-28
 

Piekarowicz, A., Bujnicki JM

 [pdf]
Cloning of the Dam methyltransferase gene from Haemophilus influenzae bacteriophage HP1.
Acta Microbiol Pol 1999 48(2):123-129.

 

Papers in Polish (4 invited review articles and book chapters).

 

Bujnicki JM, Ginalski K, Kolinski A, Kosinski J

 [pdf]
[Odgadywanie struktur zycia]
Scientific American, Polish edition [Swiat Nauki], 2006, 2, 174
 

Turkiewicz M, Bialkowska A, Tkaczuk KL, Kaluzewska M, Makowski K, Cieslinski H, Wanarska M, Kur J, Bujnicki JM

 [pdf - not available]
[Antarktyczna beta-galaktozydaza - wlasciwosci i wykorzystanie w hydrolizie laktozy]
chapter 18 in [Enzymatyczna modyfikacja skladnikow zywnosci], 2005. Editors, Kolakowski E, Bendarski W, Bielecki S.
 

Bujnicki JM

 [pdf]
[Przewidywanie struktury bialek: Boltzmann i Darwin]
Kosmos, 2005, 54, 155-162
 

Cymerman IA, Sasin JM, Bujnicki JM

 [pdf]
[Przewidywanie struktury bialek: od modelowania opartego na szablonach do rekombinacji fragmentow metoda Frankensteina].
In [Na pograniczu Chemii i Biologii], vol X, 2004. Editors, Koroniak H, Barciszewski J