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
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  • 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 bioinformatics software development
for crosslinking-based stabilization of proteins

 

Deadline for applications:  January 31st, 2023. Preferred job starting date: March 1st, 2023 or as soon as possible

 

As a Researcher, you will play a leading role in the development and application of software for computational design of chemical cross-linking strategies that aim for stabilization of protein 3D structures for for biotechnological and biomedical applications. In particular, you will be involved in the development of new software, optimization of existing software, in the design and optimization of computational workflows. The goal of your work will be to develop and test software for the development of improved protein variants that have real-life application in biotechnology.

 

This position is funded by the TRANSITION grant INCYPROnext from the European Innovation Council, Horizon Europe, which supports bilateral collaboration between Incircular B.V., a spin-off founded by the Vrije Universiteit Amsterdam (coordinator), and the International Institute of Molecular and Cell Biology in Warsaw (academic collaborator).
The project aims to improve and commercialize INCYPRO, the innovative protein stabilization technology invented and developed in Prof. Grossman's research lab at VUA, with the macromolecular modeling expertise of Prof. Bujnicki's lab at IIMCB. The Grossman and Bujnicki teams have already collaborated scientifically and published a joint paper. The goal of the INCYPROnext grant is to provide a key technology for stabilizing proteins in therapeutics and diagnostics that will enable applications that were not previously possible.

 

The position in the INCYPROnext project is ideal for you if you have solid experience both in software development (in particular in C/C++) and in macromolecular modeling (in particular Monte Carlo and/or Molecular Dynamics simulations), and if you wish to learn new techniques of integrative structural biology, including the application of chemical cross-linking to control macromolecular dynamics and stability of 3D structures in adverse conditions. You must be an experienced programmer and modeler by the time you start the project so that you can read and modify existing advanced code under the supervision of other programmers who have experience with this code. This position is not intended for beginners who want to get started in software development or macromolecular modeling, but for experienced programmers and modelers who are motivated to develop their skills in the context of collaboration between academia and industry. We encourage applications from candidates with at least a few years of postdoctoral experience and with extensive experience in both structural bioinformatics software development and molecular simulation with macromolecules and distance constraints.

 

Applications from candidates interested in long-term collaboration beyond the INCYPROnext project will have an advantage. Since the INCYPROnext project offers a relatively short-term position, we encourage applicants interested in submitting their own grant/funding applications for projects of mutual scientific interest to support a much longer collaboration. Candidates should be willing to take a leadership role and submit a grant/scholarship application within their first 6-12 months of employment with a project that connects the area of our interests.

 

We offer:

• Full-time contract (“umowa o pracę”) for at least 7 months, with an intended extension depending on performance and applications for extramural funding. This project provides funding until May 2024 t the latest, and we are looking for applicants who can successfully obtain their own funding to continue our collaboration beyond that date.

• Gross monthly remuneration starting at 10,000 PLN/month, commensurate with experience (the final monthly gross salary will be calculated individually during the employment process, taking into account the length of contract). Offered renumeration includes 13th salary after working for the Institute for six months in a given calendar year, and may be supplemented by additional bonuses such as yearly bonus, and other Social Fund financial benefits.

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

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

• Administrative and organizational support from professional English-speaking personnel

 

We require:

• Ph.D. in any area relevant to the project (e.g., structural biology, physics, biology, chemistry, etc.)

• Strong publication record, including at least one first-author publication in a good journal

• Documented experience in molecular simulations

• Documented experience in programming: Python is a must, C/C++ is advantageous

• Experience in structural bioinformatics is not essential, but will be a strong advantage

• Experience in machine learning is not essential, but will be a strong advantage

• Expertise and competence in designing and carrying out computational analyses of complex datasets and in interpreting their results

• Experience in writing manuscripts for publication, and fellowship or grant proposals

• Vision of your professional growth within ~3-5 years, including the capacity to apply for fellowship/grant funding within the first year of your employment, with projects that synergize the core strengths of the team with your own ideas

• 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-researcher-INCYPRO" 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 explicit responses to the following questions: What are scientific interests and how do they relate to requirements of the position offered? What are key strengths? What do know about our laboratory, why do want to work with us, what would you like to learn while working with us?,
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. In this competition we intend to recruit up to two candidates. The competition may be extended or repeated until suitable candidates who fulfill all requirements are found.

Specialist Position

bioinformatics software developer / data analyst

 

Deadline for applications:  January 31st, 2023. Preferred job starting date: March 1st, 2023 or as soon as possible

 

As a Specialist, you will be involved in the development of bioinformatics software, in particular programs for bioinformatics data analysis. The main goal of the work will be to integrate various programs developed in the team and third-party software, as well as maintenance and further development of the existing workflows. You will be also involved in the development of tools for task automation and house-keeping. You will be also involved in research projects, including bioinformatics data analyses. In such a case, as a contributor to research and software development, you may co-author scientific publications describing the relevant research.

 

This position is ideal for you if you are a junior bioinformatician, interested in developing bioinformatics software for handling data related to RNA sequences, structures, and interactions, improving your skills while working in an interdisciplinary team, together with experienced software developers, molecular modelers, and experimental biologists.

 

We offer:

• Full-time contract (“umowa o pracę”) initially for 14 months (a period covered by a research grant), with an intended long-term extension depending on performance

• Gross salary starting at ~5350 PLN/month with social security. Additional 13th salary after working a minimum of six months in a given calendar year

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

• Scientific training, support from peers

• Administrative and organizational support from professional English-speaking personnel

 

We require:

• M.Sc. degree (or equivalent) in biology, chemistry, physics, mathematics, computer science, or related area.

• Documented proficiency in programming in Python 2.7 / 3.8+ is essential. Candidates are requested to provide samples of their Python code.

• Hands-on experience with software development tools and practices (git/github or other version control systems, unit testing, code reviews, etc.) is required

• At least basic experience in bioinformatics is required

• Programming in C/C++ is an advantage, but not required. Experience with other programming languages is an advantage. Applicants are asked to provide examples of their code for each language and programming skill they claim.

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

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

 

How to apply:

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

• In the subject of the message include "IIMCB-specialist-bioinfo" 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 successes, and your key software/web development projects you are most proud of, 3) contacts to at least two potential referees. 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 competition may be extended or repeated until a suitable candidate who fulfills all requirements is found

 

The Specialist 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 candidate will join the project entitled “Integrative modeling and structure determination of macromolecular complexes comprising RNA and protein” which is carried out as the MAESTRO 2017/26/A/NZ1/01083 grant of the Polish National Science Centre.