Bujnicki lab - Employment
  • 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

red - jobs focused on software development (with some molecular modeling)
orange - jobs focused on modeling and data analyses (with some software development)
green - jobs focused on experimental biochemistry and biophysics

Laboratory of Bioinformatics and Protein Engineering at the International Institute of Molecular and Cell Biology (IIMCB), Warsaw, headed by Prof. Janusz M. Bujnicki, offers a position for a

 

 

 

Postdoctoral Researcher

in experimental structural biology of RNA

 

Deadline for applications: September 28th, 2023. Preferred job starting date: November 2nd, 2023 or as soon as possible

 

As a Postdoctoral Researcher, you will be involved in interdisciplinary analyses of RNA structure focused on mechanistic, structure-level understanding of how posttranscriptional modifications influence RNA folding and its ability to form alternative 3D structures.

 

This position is ideal for you if you have solid experience in experimental structural biology (for proteins and/or nucleic acids) or in the analysis of RNA modifications. We are also interested in applications from candidates with experience in other areas related to experimental studies of RNA structure, who can contribute new techniques to be used in our interdisciplinary work. We are looking for applicants interested in applying for extramural grants or fellowships.

 

We offer:

• Full-time contract (“umowa o pracę”) for at least 18 months, with an intended extension depending on performance and applications for extramural funding.

• Gross monthly remuneration approx. 8100 PLN/month (the final monthly gross salary will be calculated individually during the employment process, taking into account the length of service). Additional bonuses such as the 13th salary after working for the Institute for six months in a given calendar year, or Christmas bonus may supplement this salary.

• Benefits including reduced-rate for an individual medical care package and membership in the MultiSport program

• Work in a multidisciplinary, international team, in a dynamic organization, with multiple opportunities for professional development, participation in courses, scientific training and academic mentoring

• Administrative and organizational support from professional English-speaking personnel

 

We require:

• Ph.D. in any relevant area (e.g., biology, chemistry, etc.), defended no more than 7 years before the start of the contract (according to the rules of the funding agency).

• Fulfillment of formal criteria of the competition in particular section 2.1.1: https://tinyurl.com/5em5kbah

• Experience related to at least one of the following areas: experimental structure determination of biological macromolecules (e.g., cryo-EM, X-ray crystallography, experimental molecular biology of RNA (e.g., NGS-based methods), or biophysical analyses of macromolecular structure and dynamics

• approach to achieving objectives, good interpersonal skills, collaborative and adaptive attitude

• Very good organizational skills, especially project and time management skills

• Very good command of English (written and oral communication) and presentation skills

 

How to apply:

• Email your application to recruitment@iimcb.gov.pl  

• In the subject of the message include "IIMCB-postdoc-structural-biologist" and your first and last name

• application must be submitted in English and should contain: 1) a CV, 2) a cover letter including a short description of key achievements and expertise how they relate to the position offered, 3) contacts to at least two potential referees, including Ph.D. . At this stage, please do not attach copies of diplomas, .

• Please include the following statement in CV: “I hereby agree to the processing of my personal data, included in the application documents by the International Institute of Molecular and Cell Biology in Warsaw, 4 Księcia Trojdena Street, 02-109 Warsaw, for the purpose of carrying out the current recruitment process.” data will the recruitment procedure by the International Institute of Molecular and Cell Biology in Warsaw. Full information is available under the link https://bit.ly/3UFWpY2

• We will contact only selected best candidates, who may be given additional questions and tasks as a part of the recruitment process

 

The Postdoctoral Researcher will be selected from candidates in an open competition, according to the procedure complying with the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research strategy https://tinyurl.com/54meyr6r. The competition may be extended or repeated until suitable candidates who fulfill all requirements are found.

 

This position is offered within a project entitled “Unraveling the influence of posttranscriptional modifications on RNA 3D structure formation and its dynamics, with the integrated use of theoretical and experimental approaches” carried out as the OPUS grant of the Polish National Science Centre (UMO-2020/37/B/NZ2/02456).

 

 

Postdoctoral researcher

in software development and modeling of RNA and RNP 3D structure

 

Deadline for applications: September 28th, 2023. Preferred job starting date: November 2nd, 2023 or as soon as possible

 

As a Postdoctoral Researcher, you will play a pivotal role in the development of software for the computational determination and modeling of macromolecular structures of RNA and proteins. Specifically, you will contribute to the development of our highly regarded SimRNA and SimRNP methods for modeling RNA and RNP structures. This will encompass both purely theoretical simulations and data from various experiments, notably cryo-EM.

 

This position is a perfect fit for individuals with substantial experience in software development (especially in C/C++) and macromolecular modeling. It's essential that you are a proficient programmer, enabling you to understand and adapt the existing advanced code. This role is tailored for adept programmers eager to hone their skills further, rather than beginners looking to embark on software development.

 

We offer:

• Full-time contract (“umowa o pracę”) for at least 15 months, with an intended extension depending on performance and applications for extramural funding.

• Gross monthly remuneration approx. 8100  PLN/month (the final monthly gross salary will be calculated individually during the employment process, taking into account the length of service). Additional bonuses such as the 13th salary after working for the Institute for six months in a given calendar year, or Christmas bonus may supplement this salary.

• Benefits including reduced-rate for an individual medical care package and membership in the MultiSport program

• Work in a multidisciplinary, international team, in a dynamic organization, with multiple opportunities for professional development, participation in courses, scientific training and academic mentoring

• Administrative and organizational support from professional English-speaking personnel

 

We require:

• Ph.D. in any relevant area (e.g., biology, chemistry, physics, computer science etc.) defended no more than 7 years before the start of the contract (according to the rules of the funding agency).

• Fulfillment of formal criteria of the competition https://shorturl.at/AIN36 (p. 59, only in PL version)

• Documented experience in programming (C/C++ or Python and ideally both)

• Experience related to at least one of the following areas: structural bioinformatics, molecular simulations, machine learning, RNA structure analysis

• approach to achieving objectives, good interpersonal skills, collaborative and adaptive attitude

• Very good organizational skills, especially project and time management skills

• Very good command of English (written and oral communication) and presentation skills

 

How to apply:

• Email your application to recruitment@iimcb.gov.pl  

• In the subject of the message include "IIMCB-postdoc-programmer-3Dmodeling" and your first and last name

• application must be submitted in English and should contain: 1) a CV, 2) a cover letter including a short description of key achievements and expertise how they relate to the position offered 3) contacts to at least two potential referees, including Ph.D. . At this stage, please do not attach copies of diplomas, .

• Please include the following statement in CV: “I hereby agree to the processing of my personal data, included in the application documents by the International Institute of Molecular and Cell Biology in Warsaw, 4 Księcia Trojdena Street, 02-109 Warsaw, for the purpose of carrying out the current recruitment process.” data will the recruitment procedure by the International Institute of Molecular and Cell Biology in Warsaw. Full information is available under the link https://bit.ly/3UFWpY2

• We will contact only selected best candidates, who may be given additional questions and tasks as a part of the recruitment process

 

The Postdoctoral Researcher will be selected from candidates in an open competition, according to the procedure complying with the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research strategy https://tinyurl.com/54meyr6r. The competition may be extended or repeated until suitable candidates who fulfill all requirements are found.

 

The first 11 months of employment at this position will be funded by the MAESTRO grant of the Polish National Science Centre (2017/26/A/NZ1/01083), which supports the project entitled “Integrative modeling and structure determination of RNA-protein complexes.”

 

 

Postdoctoral Researcher

in RNA bioinformatics

 

Deadline for applications: September 28th, 2023. Preferred job starting date: November 2nd, 2023 or as soon as possible

 

As a Postdoctoral Researcher, you will be involved in interdisciplinary analyses of RNA structure focused on mechanistic, structure-level understanding of how posttranscriptional modifications influence RNA folding and its ability to form alternative 3D structures.

 

This position is ideal for you if you have solid experience in bioinformatics and computational biology, in particular in structural bioinformatics of RNA. We are also interested in applications from candidates with experience in other areas of computational biology, in particular software development, who can contribute to be our interdisciplinary work on RNA structure.

 

We offer:

• Full-time contract (“umowa o pracę”) for at least 18 months, with an intended extension depending on performance and applications for extramural funding.

• Gross monthly remuneration approx. 8100 PLN/month (the final monthly gross salary will be calculated individually during the employment process, taking into account the length of service). Additional bonuses such as the 13th salary after working for the Institute for six months in a given calendar year, or Christmas bonus may supplement this salary.

• Benefits including reduced-rate for an individual medical care package and membership in the MultiSport program

• Work in a multidisciplinary, international team, in a dynamic organization, with multiple opportunities for professional development, participation in courses, scientific training and academic mentoring

• Administrative and organizational support from professional English-speaking personnel

 

We require:

• Ph.D. in any relevant area (e.g., biology, computer science, etc.), defended no more than 7 years before the start of the contract (according to the rules of the funding agency).

• Fulfillment of formal criteria of the competition in particular section 2.1.1: https://tinyurl.com/5em5kbah

• Experience related to at least one of the following areas: RNA bioinformatics, molecular modeling including computational simulations of macromolecular structure and dynamics, or software development for the analysis of biological sequences and structures

• approach to achieving objectives, good interpersonal skills, collaborative and adaptive attitude

• Very good organizational skills, especially project and time management skills

• Very good command of English (written and oral communication) and presentation skills

 

How to apply:

• Email your application to recruitment@iimcb.gov.pl  

• In the subject of the message include "IIMCB-postdoc-RNA-bioinformatics" and your first and last name

• application must be submitted in English and should contain: 1) a CV, 2) a cover letter including a short description of key achievements and expertise how they relate to the position offered, 3) contacts to at least two potential referees, including Ph.D. . At this stage, please do not attach copies of diplomas, .

• Please include the following statement in CV: “I hereby agree to the processing of my personal data, included in the application documents by the International Institute of Molecular and Cell Biology in Warsaw, 4 Księcia Trojdena Street, 02-109 Warsaw, for the purpose of carrying out the current recruitment process.” data will the recruitment procedure by the International Institute of Molecular and Cell Biology in Warsaw. Full information is available under the link https://bit.ly/3UFWpY2

• We will contact only selected best candidates, who may be given additional questions and tasks as a part of the recruitment process

 

The Postdoctoral Researcher will be selected from candidates in an open competition, according to the procedure complying with the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research strategy https://tinyurl.com/54meyr6r. The competition may be extended or repeated until suitable candidates who fulfill all requirements are found.

 

This position is offered within a project entitled “Unraveling the influence of posttranscriptional modifications on RNA 3D structure formation and its dynamics, with the integrated use of theoretical and experimental approaches” carried out as the OPUS grant of the Polish National Science Centre (UMO-2020/37/B/NZ2/02456).