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  • Laboratory of Bioinformatics and Protein Engineering

Laboratory of Bioinformatics and Protein Engineering

 bujnicki j

Janusz M. Bujnicki, PhD, Professor 

Correspondence address:
Laboratory of Bioinformatics and Protein Engineering
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www: iimcb.genesilico.pl
tel: +48 (22) 597 0750; fax: +48 (22) 597 0715


2009 - Professor of Biological Sciences, nomination by the President of the Republic of Poland
2005 - DSc Habil in Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
2001- PhD in Biology, University of Warsaw, Faculty of Biology, Poland
1998 - MSc in Microbiology, University of Warsaw, Faculty of Biology, Poland


2002-present - Professor, Head of Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Poland (100% appointment)
2019-present - Scientific Advisor, Łukasiewicz Research Network - PORT Polish Center for Technology Development (25% appointment)
2006-2020 - Associate Professor (extraordinarius), Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
2010-2011 - Deputy Director, International Institute of Molecular and Cell Biology in Warsaw (1 year rolling position)
2008 - Visiting Professor, University of Tokyo, Japan(sabbatical)
2004-2006 - Assistant Professor, Adam Mickiewicz University, Poznań, Poland
2001 - Visiting Scientist, National Center for Biotechnology Information,National Institutes of Health, Bethesda, Maryland, USA
1999-2002 - Research Scientist, Bioinformatics Laboratory, International Institute of Molecular and Cell Biology in Warsaw, Poland
1998-2000 - Senior Research Assistant, Henry Ford Hospital, Detroit, Michigan, USA


2019-2022 - Member, Committee for Science Evaluation, Ministry of Science and Higher Education
2020 - Member, Advisory Group on Preventing, Counteracting and Combating COVID-19, Ministry of Science and Higher Education
2019-present - Member, University Council, University of Warsaw (Chairman, 2019-2020)
2018-present - Member, Academia Europaea
2018-present - Member, European Molecular Biology Organization
2017-present - Member, European Science Advisors Forum
2016-present - Corresponding Member, Polish Academy of Sciences
2016-2017 - Member, Council of the National Science Congress
2015-2020 - Member, Group of Chief Scientific Advisors, European Commission’s Scientific Advice Mechanism
2014-2018 - Member, Scientific Policy Committee, Polish Ministry of Science and Higher Education
2013-present - Executive Editor, Nucleic Acids Research
2013-2016 - Member, Scientific Committee of the Innovative Medicines Initiative
2013-2015 - Member, Science Europe: Life, Environmental and Geo Sciences (LEGS) Scientific Committee
2011-2016 - Member, Polish Young Academy, Polish Academy of Sciences
2007-present - Member, Polish Bioinformatics Society (founding member; Vice-President, 2007-2010; President, 2011-2013)
2007-present - Member, RNA Society
2001-present - Member, International Society for Computational Biology (Senior Member, 2015-)


2019 - André Mischke Young Academy of Europe Prize for Science and Policy Honorary Award "For Merits for Inventiveness," Prime Minister at the request of the Polish Patent Office
2019 - Award for Organizational Achievements, Ministry of Science and Higher Education
2017 - Crystal Brussels Sprout Award
2015 - Jan Karol Parnas Award of the Polish Biochemical Society
2014 - National Science Centre Award for outstanding scientific achievements
2014 -Master Award, Foundation for Polish Science
2014 - Prime Minister’s Award for outstanding scientific achievements
2014 - Selected as one of “25 leaders for the next 25 years” by Teraz Polska magazine of the Polish Promotional Emblem Foundation
2014 - Knight's Cross of the Order of Polonia Restituta
2014 - Award in the Science category of the national plebiscite “Poles with Verve”
2013 - ERC Proof of Concept Grant
2012 - Award for Outstanding Research Achievements, Ministry of Science and Higher Education
2010 - ERC Starting Grant (2011-2015)
2009 - Scholarship for Outstanding Young Scientists, Minister of Science and Higher Education
2009 - Award for Research Achievements, Ministry of Science and Higher Education
2006 - Prime Minister Award for habilitation thesis
2006 - Young Researcher Award in Structural and Evolutionary Biology, Visegrad Group Academies of Sciences
2003, 2004 - START Scholarship for Young Scientists, Foundation for Polish Science
2002-2005 - EMBO/HHMI Young Investigator Award
2002 - Award for best Polish genetics-related publication in 2002, Polish Genetics Society
2001 - Award for best Polish publication on nucleic acid biochemistry in 2000, Polish Biochemical Society and Sigma-Aldrich


A. Żylicz-Stachula, A. Chmiel, I. Cymerman, A. Czerwoniec, M. Gajda, M. Pawłowski, J. Sasin-Kurowska, J. Kosiński, A. Obarska-Kosińska, S. Pawlak, E. Purta, K. Tkaczuk, Ł. Kościński, M.Rother, W. Potrzebowski, I. Korneta, T. Puton, J. Kasprzak, I. Tuszyńska, Ł. Kozłowski, M. Werner, A. Kamaszewska, A. Philips, K. Milanowska, M. Piętal, D. Matelska, K. Majorek, M. Domagalski, T. Osiński, M. Machnicka, M. Magnus, K. Szczepaniak, M. Zielińska, Astha, I. Foik, D. Toczydłowska-Socha.

Our group is involved in theoretical and experimental research on sequence structure-function relationships in proteins, nucleic acids, and macromolecular complexes. Theoretical research involves the development of computer software for the analysis of biological macromolecules. We are currently focusing on developing software for the structural prediction and modeling of RNA and RNA protein complexes. To date, we have developed and made publicly available one of the first methods for the automated comparative (template-based) modeling of three-dimensional (3D) RNA structures (ModeRNA; http://iimcb. genesilico.pl/moderna/) and a method for de novo (template-free) RNA structure modeling (SimRNA; http://genesilico.pl/software/stand-alone/simrna, also available as a web server at http://genesilico. pl/SimRNAweb). We also developed a method for predicting metal ion binding sites in RNA structures (MetalionRNA; http://metalionrna.genesilico.pl), a method for modeling RNA-ligand complexes, and a method for predicting the structure of RNA-protein complexes (http://genesilico.pl/NPDock). Other methods for RNA bioinformatics include a method for the classification of contacts in RNA 3D structures (ClaRNA; http://iimcb.genesilico.pl/clarna/) and a method for the flexible superposition of RNA 3D structures and their fragments (SupeRNAlign; http:// genesilico.pl/supernalign/). We also developed various databases, including a database of RNA modification pathways and enzymes (MODOMICS; http://modomics. genesilico.pl) and a database of RNA 3D motifs and their interactions (RNA Bricks; http://iimcb.genesilico.pl/rnabricks/). 

Our suite of programs for the prediction and analysis of protein structures and macromolecular complexes includes the GeneSilico MetaServer (https://www.genesilico.pl/meta2/), methods for modeling large macromolecular complexes with the use of restraints that are derived from experimental data (PyRy3D, http://genesilico.pl/pyry3d/; MinkoFit3D, http://iimcb.genesilico.pl/minkofit3d/), and a method for discriminating models according to their agreement with experimental data (FILTREST3D; http://filtrest3d.genesilico.pl/). We also developed methods for predicting order/ disorder in protein structures (http://iimcb. genesilico.pl/metadisorder/).

Our experimental research focuses on elucidating sequence structure-function relationships in bio-macromolecules (currently mainly RNA and RNA-protein complexes, also with small chemical molecules) using biophysics, biochemistry, molecular biology, and cell biology. We tightly integrate theoretical and experimental research. We often experimentally test functional and structural predictions for RNAs, proteins, and their complexes that are obtained using computational methods. For structural studies, we combine X-ray crystallography and low-resolution methods, such as small-angle X-ray scattering (SAXS), structure probing by chemical modification or crosslinking, mass spectrometry, circular dichroism, mutagenesis, etc. Most recently, our group began using cryo-EM. We have collected our first datasets and began developing software for interpreting the data.


Matching tRNA modifications in humans to their known and predicted enzymes he acquisition of post-transcriptional chemical modifications is an essential part of the maturation process, required to generate functional tRNA molecules. Modifications play different roles in controlling the stability, folding, and decoding properties of tRNAs and can be determinants or antideterminants of other components of the translation apparatus, such as aminoacyl-tRNA synthetases. Additionally, tRNA modifications can be recognition elements of ribonucleases, leading to the generation of tRNA fragments that affect multiple cellular processes. However, very few modifications (e.g., m1G37, Ψ55, and t6A37) are present at a specific position of a particular tRNA in (almost) all known organisms. Most of them are specific to particular taxons, from species to kingdoms. For example, lysidine (k2C34) is a hallmark of bacteria, whereas archaeosine (G+15) is only found in archaea. Depending on the organism, the total number of genes that encode tRNA modification enzymes varies from 11 in some obligate symbionts to ~100 in humans, of which 50 are currently represented in MODOMICS, the main database of RNA modification pathways that was developed and is maintained by the Bujnicki group at IIMCB, in collaboration with various groups worldwide (http://modomics.genesilico.pl).

The near complete sets of tRNA modification genes are currently available for only one organism per domain of life: Saccharomyces cerevisiae for eukarya (where only one gene that is required for the formation of ncm5U out of cm5U is missing), Escherichia coli for bacteria (where only the genes for ho5U34 and Acp3U47 formation remain unidentified), and Haloferax volcanii for archaea (where a handful of genes are missing). Beyond these three organisms, the annotation of tRNA modification genes remains scarce because of difficulties in connecting various RNA modification enzymes, which often exhibit complex evolutionary relationships, with various modifications that are present in tRNAs. It has been difficult to identify enzymes that are responsible for many tRNA modifications and hence to determine the function of those tRNA modifications in many species, including humans.

Recently, an increasing number of mutations that cause genetic diseases have been mapped to human genes that encode tRNA modification enzymes, thus making a comprehensive list of these genes highly desirable. In a collaborative effort with Valerie de Crécy-Lagard and her team at the University of Florida, Sebastian Leidel and his team at the University of Bern (previously MPI Muenster and University of Muenster), and Todd Lowe at the University of California, Santa Cruz, we compiled a comprehensive list of known and predicted tRNA modifications in Homo sapiens with genes that are implicated in their biosynthesis. This analysis allowed the identification of remaining gaps in knowledge in the field of human tRNA modifications and will help guide future experiments. Furthermore, we have used publicly available datasets to determine the expression profiles and proteomic evidence of known and predicted modification enzymes. Our work will facilitate access to the current knowledge on human tRNA modification enzymes for a wider community of biologists. These results were published in Nucleic Acids Research (de Crécy-Lagard et al., 2019).

Ongoing work: new bioinformatics methods for predicting structures of RNA-protein complexes

RNA-protein (RNP) interactions play pivotal roles in various biological processes, such as protein synthesis, the regulation of gene expression, RNA splicing, transport, storage, and stabilization. To understand the functional and mechanistic details of these processes, it is essential to have information about the 3D structures of these complexes. The inherent flexibility of RNA molecules and transient nature of these complexes make it technically difficult to determine these structures experimentally. In addition to experimental work, our laboratory develops methods for theoretical predictions.

One of our recent developments is SimRNP, a variant of SimRNA that enables the modeling of interactions between RNA and other types of molecules, in this case proteins. The representation of RNA and statistical potential for RNA are essentially the same, whereas the representation of protein molecules is very similar to the coarse-grained model and statistical potential that are used in the REFINER program for protein folding (developed earlier by Michał Boniecki). Additionally, a statistical potential for RNA-protein interactions was introduced based on an analysis of high-resolution structures of RNAprotein complexes. A typical task for SimRNP is to predict the 3D structure of an RNP complex, starting from an unbound structure of the protein and RNA components or from an unbound protein structure and unfolded RNA sequence. Protein components are typically partially restrained to maintain the protein fold, but conformational changes are allowed to reflect induced fit upon RNA-protein binding.

If the structures of both components (RNA and protein) are available, then the RNP complex structure can be predicted by docking, in which conformational sampling can be separated from scoring of the conformations that are obtained. The existing docking methods can be broadly classified as rigid docking algorithms that do not account explicitly for conformational changes and flexible docking algorithms that attempt to account for conformational changes. Major challenges in RNP docking are molecular flexibility and computational complexity that are associated with flexible docking. Generating conformations that are similar to the bound conformation from the starting structures and discriminating them from others is a challenging task. We developed a prototypical meta-predictor for RNA-protein docking, which combines various existing methods for docking and scoring to obtain biologically, chemically, and physically relevant predictions. Such meta-predictions were successfully applied previously to model protein structures and protein-protein docking. RNP docking is performed using different methods, and the top-scoring docking poses from each of these are rescored using different scoring functions. If the scoring methods reach a consensus, then decoys that are obtained from different methods are clustered together. However, in the absence of consensus scoring, top models that are proposed by different methods are suggested as alternative solutions. The MetaRNPDock metaserver is available at http://genesilico.pl/metaRNPDock/ (co-authors: Nithin Chandran, Sunandan Mukherjee, Pietro Boccaletto, Michał J. Boniecki, and Janusz M. Bujnicki).


Lab Leader:

  • Janusz M. Bujnicki, PhD, Professor

Senior Researchers:

  • Elżbieta Purta, PhD

  • Filip Stefaniak, PhD


  • Michał Boniecki, PhD

Postdoctoral Researchers:

  • Belisa R. H. de Aquino, PhD

  • Sunandan Mukherjee, PhD

  • Giorgos Kritkos, PhD

  • Almudena Ponce Salvatierra, PhD

  • Tales Rocha de Moura, PhD

  • Tomasz Wirecki, PhD

Research Assistants:

  • Katarzyna Merdas, MSc

  • Agata Bernat, MSc

  • Małgorzata Kurkowska, MSc

Research Technicians:

  • Radosław Giziński, MSc

  • Enda Farell, MSc

  • Ytalia Lavalle, BSc

PhD Students:

  • Nagendar Goud Badepally, MSc

  • Masoud Amiri Farsani, MSc

  • Farhang Jaryani, PhD

  • Seyed Naeim Moafinejad, MSc

  • Andrea Capannini, MSc

Lab Technician:

  • Iwona Ptasiewicz (part-time)

Laboratory Support Specialist:

  • Katarzyna Grzelak, MSc


Salerno-Kochan A, Horn A, Ghosh P, Nithin C, Kościelniak A, Meindl A, Strauss D, Krutyhołowa R, Rossbach O, Bujnicki JM, Gaik M, Medenbach J, Glatt S.

Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26.

Szulc NA, Mackiewicz Z, Bujnicki JM, Stefaniak F.

fingeRNAt-A novel tool for high-throughput analysis of nucleic acid-ligand interactions.

Boccaletto P, Stefaniak F, Ray A, Cappannini A, Mukherjee S, Purta E, Kurkowska M, Shirvanizadeh N, Destefanis E, Groza P, Avşar G, Romitelli A, Pir P, Dassi E, Conticello SG, Aguilo F, Bujnicki JM.

MODOMICS: a database of RNA modification pathways. 2021 update.

Mohammadi-Arani R, Javadi-Zarnaghi F, Boccaletto P, Bujnicki JM, Ponce-Salvatierra A.

DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes.


Ponce-Salvatierra A, Boccaletto P, Bujnicki JM.

DNAmoreDB, a database of DNAzymes.

Koralewska N, Szczepanska A, Ciechanowska K, Wojnicka M, Pokornowska M, Milewski MC, Gudanis D, Baranowski D, Nithin C, Bujnicki JM, Gdaniec Z, Figlerowicz M, Kurzynska-Kokorniak A.

RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity.

Stefaniak F, Bujnicki JM.

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.

Wegrzyn K, Zabrocka E, Bury K, Tomiczek B, Wieczor M, Czub J, Uciechowska U, Moreno-Del Alamo M, Walkow U, Grochowina I, Dutkiewicz R, Bujnicki JM, Giraldo R, Konieczny I.

Defining a novel domain that provides an essential contribution to site-specific interaction of Rep protein with DNA.

Kuepper A, McLoughlin NM, Neubacher S, Yeste-Vázquez A, Collado Camps E, Nithin C, Mukherjee S, Bethge L, Bujnicki JM, Brock R, Heinrichs S, Grossmann TN.

Constrained peptides mimic a viral suppressor of RNA silencing.


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

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.

Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z.

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.

Lambert AR, Hallinan JP, Werther R, Głów D, Stoddard BL.

Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.

Miao Z et al. (Boniecki MJ, Bujnicki JM, Joshi A, Magnus M, Piatkowski P, Pluta R.)

RNA-Puzzles Round IV: 3D Structure Predictions of Four Ribozymes and Two Aptamers.

Wirecki TK, Merdas K, Bernat A, Boniecki MJ, Bujnicki JM, Stefaniak F.

RNAProbe: a web server for normalization and analysis of RNA structure probing data.

Andryianau G, Kowalski M, Piotrowicz MC, Rajkiewicz AA, Dymek B, Sklepkiewicz PL, Pluta E, Stefaniak F, Czestkowski W, Olejniczak S, Mazur M, Niedziejko P, Koralewski R, Matyszewski K, Gruza M, Zagozdzon A, Salamon M, Rymaszewska A, Welzer M, Dzwonek K, Golab J, Olczak J, Bartoszewicz A, Golebiowski A.

Benzoxazepine-Derived Selective, Orally Bioavailable Inhibitor of Human Acidic Mammalian Chitinase.

Brzuzan P, Mazur-Marzec H, Florczyk M, Stefaniak F, Fidor A, Konkel R, Woźny M.

Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea.


Ponce-Salvatierra A, Astha, Merdas K, Chandran N, Ghosh P, Mukherjee S, Bujnicki JM.

Computational modeling of RNA 3D structure based on experimental data.

Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I.

Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.

Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ.

Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.

Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM.

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

Magnus M, Kappel K, Das R, Bujnicki JM

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

Radom M, Machnicka MA, Krwawicz J, Bujnicki JM, Formanowicz P

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

The RNAcentral Consortium (Bujnicki JM, Boccaletto P)

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

Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM.

QRNAS: software tool for refinement of nucleic acid structures.

de Crecy-Lagard V, Boccaletto P, Mangleburg C, Sharma P, Lowe T, Leidel S, Bujnicki JM.

Matching tRNA modifications in humans to their known and predicted enzymes.

Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S.

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

Sulej AA

Improving selectivity of DNA-RNA binding zinc finger using directed evolution.

Mazur M, Dymek B, Koralewski R, Sklepkiewicz P, Olejniczak S, Mazurkiewicz M, Piotrowicz M, Salamon M, Jędrzejczak K, Zagozdzon A, Czestkowski W, Matyszewski K, Borek B, Bartoszewicz A, Pluta E, Rymaszewska A, Mozga W, Stefaniak F, Dobrzański P, Dzwonek K, Golab J, Golebiowski A, Olczak J.

Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases.


Pluta R, Espinosa M.

Antisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs.

Foik IP, Tuszynska I, Feder M, Purta E, Stefaniak F, Bujnicki JM.

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

Kumari P, Aeschimann F, Gaidatzis D, Keusch JJ, Ghosh P, Neagu A, Pachulska-Wieczorek K, Bujnicki JM, Gut H, Großhans H, Ciosk R.

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

Nithin C, Ghosh P, Bujnicki JM.

Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes.

Fernandes H, Czapinska H, Grudziaz K, Bujnicki JM, Nowacka M.

Crystal structure of human Acinus RNA recognition motif domain.

Toczydlowska-Socha D, Zielinska MM, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM.

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

Jantsch MF et al. (Bujnicki J, Purta E)

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU.

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

Mazur M, Bartoszewicz A, Dymek B, Salamon M, Andryianau G, Kowalski M, Olejniczak S, Matyszewski K, Pluta E, Borek B, Stefaniak F, Zagozdzon A, Mazurkiewicz M, Koralewski R, Czestkowski W, Piotrowicz M, Niedziejko P, Gruza MM, Dzwonek K, Golebiowski A, Golab J, Olczak J.

Discovery of selective, orally bioavailable inhibitor of mouse chitotriosidase.

Boccaletto P, Magnus M, Almeida C, Zyla A, Astha A, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki TK, Boniecki MJ, Stefaniak F, Bujnicki JM.

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

Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM.

MODOMICS: a database of RNA modification pathways. 2017 update.


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

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

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

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

Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I

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

Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M

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

Piątkowski P, Jabłońska J, Żyła A, Niedziałek, Matelska D, Jankowska E, Waleń T, Dawson WK, Bujnicki JM.

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

Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L.

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

Dzananovic E, Astha, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA.

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


Magnus MM, Boniecki MJ, Dawson WK, Bujnicki JM

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

Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I

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

Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S

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

Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, Valpuesta J

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM

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

Dawson WK, Bujnicki JM

Computational modeling of RNA 3D structures and interactions

Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W

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

Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ

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

Iskierko Z, Sharma PS, Prochowicz D, Fronc K, D'Souza F, Toczydłowska D, Stefaniak F, Noworyta K

Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination.

Pawlowski M, Kozlowski L, Kloczkowski A

MQAPsingle: A quasi single-model approach for estimation of the quality of individual protein structure models

Urulangodi M, Dhanaraju R, Gupta K, Roy RP, Bujnicki JM, Rao DN

Asymmetric DNA methylation by dimeric EcoP15I DNA methyltransferase

Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs

Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM

Coarse-grained modeling of RNA 3D structure

Głów D, Nowacka M, Skowronek KJ, Bujnicki JM.

Sequence-specific endoribonucleases.


Roszczenko P, Grzeszczuk M, Kobierecka P, Wywial E, Urbanowicz P, Wincek P, Nowak E, Jagusztyn-Krynicka EK

Helicobacter pylori HP0377, a member of the Dsb family, is an untypical multifunctional CcmG that cooperates with dimeric thioldisulfide oxidase HP0231

Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet J-F, Jagusztyn-Krynicka EK

Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FHT

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

Boekema C, Owens F, Love A, Li Z, Sakkaris P, Dawson WK

A magnetic origin of cuprate superconductivity? A MaxEnt-mu SR view

Chawla M, Oliva R, Bujnicki JM, Cavallo L

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

Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM

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

Czerwoniec A, Kasprzak JM, Bytner P, Dobrychlop M, Bujnicki JM

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

Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA

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

Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM

Sequence-specific cleavage of dsRNA by Mini-III RNase

Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC

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

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

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

Philips A, Lach G, Bujnicki JM

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

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

Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631

Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM

NPDock – a web server for protein-nucleic acid docking

Zheng H, Shabalin I, Handing K, Bujnicki JM, Minor M

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

The RNAcentral Consortium (Petrov AI et al within Bujnicki JM)

RNAcentral: a comprehensive database of non-coding RNA sequences

Machnicka AM, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM.

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


Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z

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

Ramos-Molina B, Lambertos A, Lopez-Contreras AJ, Kasprzak JM, Czerwoniec A, Bujnicki JM, Cremades A, Penafiel R

Structural and degradative aspects of ornithine decarboxylase antizyme inhibitor 2

Walen T, Chojnowski G, Gierski P,Bujnicki JM,

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

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

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

Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S

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

Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM

Computational modeling of protein-RNA complex structures

Plotka M, Kaczorowska AK, Stefanska A, Morzywolek A, Fridjonsson OH, Dunin-Horkawicz S, Kozlowski L, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T

Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins

Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K, Harding SE, Bujnicki JM, McKenna SA

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

Chojnowski G, Walen T, Bujnicki JM

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

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

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

Crochemore M, Iliopoulos CS, Kubica M, Radoszewski J, Rytter W, Stencel K, Walen T

New simple efficient algorithms computing powers and runs in strings

Sadowski Ł, Jastrzębski K, Purta E, Hellberg C, Miaczynska M

Labeling of platelet-derived growth factor by reversible biotinylation to visualize its endocytosis by microscopy

Toczyłowska-Mamińska R, Olszewska A, Laskowski M, Bednarczyk P, Skowronek K, Szewczyk A

Potassium channel in the mitochondria of human keratinocytes

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM

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

Byszewska M, Smietanski M, Purta E, Bujnicki JM.

RNA methyltransferases involved in 5' cap biosynthesis.

Machnicka M, Olchowik A, Grosjean H, Bujnicki JM.

Distribution and frequencies of post-transcriptional modifications in tRNAs.

Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M

Structural basis of the methylation specificity of R.DpnI

Rother K, Rother M, Skiba P, Bujnicki JM

Automated modeling of RNA 3D structure

Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM

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


Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H

MODOMICS: a database of RNA modification pathways: 2013 update

Milanowska K, Mikolajczak K, Lukasik A, Skorupski M, Balcer Z, Machnicka MA, Nowacka M, Rother KM, Bujnicki JM

RNApathwaysDB – a database of RNA maturation and decay pathways

Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M

Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid

Puton T, Kozlowski LP, Rother KM, Bujnicki JM

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Bujnicki JM, Tiuryn J

Bioinformatics and computational biology in Poland

Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J

RNAlyzer--novel approach for quality analysis of RNA structural models

Pawlowski M, Bogdanowicz A, Bujnicki JM

QA-RecombineIt: a server for quality assessment and recombination of protein models

Crochemore M, Iliopoulos C.S, Kociumaka T, Kubica M, Pachocki J, Radoszewski J, Rytter W,Tyczyński W, Waleń T

A note on efficient computation of all Abelian periods in a string

Bednarczyk P, Wieckowski MR, Broszkiewicz M, Skowronek K, Siemen D, Szewczyk A

Putative Structural and Functional Coupling of the Mitochondrial BKCa Channel to the Respiratory Chain

Kubica M, Kulczyńskia T, Radoszewskia J, Rytter W,Walen T

A linear time algorithm for consecutive permutation pattern matching

Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S

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

Czeredys M, Samluk L, Michalec K, Tułodziecka K, Skowronek K, Nałęcz KA

Caveolin-1 - a novel interacting partner of organic cation/carnitine transporter (octn2): effect of protein kinase C on this interaction in rat astrocytes.

Philips A, Milanowska K, Lach G, Bujnicki JM

LigandRNA: computational predictor of RNA-ligand interactions

Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP

Rational design of helical nanotubes from self-assembly of coiled-coil lock washers


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

MetalionRNA: computational predictor of metal-binding sites in RNA structures

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 DT

Structure and operation of the DNA-translocating type I DNA restriction enzymes

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

A toolbox for developing bioinformatics software

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

Computational methods for prediction of protein-RNA interactions

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

Crohn's Disease Risk Alleles on the NOD2 Locus Have Been Maintained by Natural Selection on Standing Variation

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

The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA

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

Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities

Chojnowski G, Bujnicki JM, Bochtler M

RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes

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

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

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

Crystal structures of the tRNA:m(2)G6 methyltransferase Trm14/TrmN from two domains of life

Lach G, DeKievet M, Jentschura UD

Einstein–Hopf drag, Doppler shift of thermal radiation and blackbody drag: Three perspectives on quantum friction

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 DA

Statins Impair Glucose Uptake in Tumor Cells

Samluk L, Czeredys M, Skowronek K, Nałęcz KA

Protein kinase C regulates amino acid transporter ATB

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

Crystal structure and mechanism of action of the N6-methyladenine dependent type IIM restriction endonuclease

Pietal MJ, Szostak N, Rother KM, Bujnicki JM

RNAmap2D -- calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Pawlowski M, Bujnicki JM

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement

Sulej AA, Tuszynska I, Skowronek KJ, Nowotny M, Bujnicki JM

Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger

Drozdz M, Piekarowicz A, Bujnicki JM, Radlinska M

Novel non-specific DNA adenine methyltransferases

Korneta I, Magnus M, Bujnicki JM

Structural bioinformatics of the human spliceosomal proteome

Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM

Delineation of structural domains and identification of functionally important residues in DNA repair enzyme Exonuclease VII

Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM

Rational engineering of sequence specificity in R.MwoI restriction endonuclease

Magnus M, Pawlowski M, Bujnicki JM

MetaLocGramN: A meta-predictor of protein subcellular localization for Gram-negative bacteria

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

A novel homozygous p.Arg527Leu LMNA mutation in two unrelated egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome

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

A novel insight into the oxidoreductase activity of Helicobacter pylori HP0231 protein

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

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

Korneta I, Bujnicki JM

Intrinsic disorder in the human spliceosomal proteome

Kasprzak JM, Czerwoniec A, Bujnicki JM

Molecular evolution of dihydrouridine synthases

Kozlowski LP, Bujnicki JM

MetaDisorder: A meta-server for the prediction of intrinsic disorder in proteins

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

Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling In "RNA Structure Prediction and Modelling"

Kozlowski L, Orlowski J, Bujnicki JM

Structure prediction of alternatively spliced proteins In „Alternative pre-mRNA Splicing: Theory and Protocols: The Complete Guide for Biomedical Scientists”


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

REPAIRtoire-a database of DNA repair pathways

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

RNA and protein 3D structure modeling: similarities and differences

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

ModeRNA server: an online tool for modeling RNA 3D structures

Tuszynska I, Bujnicki JM

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

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

2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family

Rother M, Rother K, Puton T, Bujnicki JM

ModeRNA: a tool for comparative modeling of RNA 3D structure

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

RNAcentral: A vision for an international database of RNA sequences

Czerwoniec A, Bujnicki JM

Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p

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

Effect of substrate features and mutagenesis of active site tyrosine residues on the reaction course catalysed by Trypanosoma brucei sterol C-24-methyltransferase

Milanowska K, Rother K, Bujnicki JM

Databases and bioinformatics tools for the study of DNA repair

Rother M, Rother K, Puton T, Bujnicki JM

RNA tertiary structure prediction with ModeRNA

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

STAT1 as a novel therapeutical target in pro-atherogenic signal integration of IFNg, TLR4 and IL-6 in vascular disease

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

Virtual screening strategies in drug design - methods and applications

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, Sc

"4D Biology for health and disease" workshop report

Husain N, Obranic S, Koscinski L, Seetharaman J, Babic F, Bujnicki JM, Maravic-Vlahovicek G, Sivaraman J

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

Kozlowski L, Orlowski J, Bujnicki JM

Structure prediction of alternatively spliced proteins

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

Template-based and template-free modeling of RNA 3D structure: inspirations from protein structure modeling

Tesfazgi Mebrhatu M, Wywial E, Ghosh A, Michiels CW, Lindner AB, Taddei F, Bujnicki JM, Van Melderen L, Aertsen A

Evidence for an evolutionary antagonism between Mrr and Type III modification systems.

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

A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase


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

FILTREST3D: discrimination of structural models using restraints from experimental data.

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

Crystal structure of a fructokinase homolog from Halothermothrix orenii

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

Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.

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

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.

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

New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA.

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

Co-evolution-driven switch of J-protein specificity towards an Hsp70 partner.

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

The YTH domain is a novel RNA binding domain.

Pukáncsik M, Békési A, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vértessy BG

Physiological truncation and domain organization of a novel uracil-DNA-degrading factor.

Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J

The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.

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

Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria.

Tuszynska I, Bujnicki JM

Predicting atomic details of the unfolding pathway for YibK, a knotted protein from the SPOUT superfamily

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

A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI).

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

IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities

Tkaczuk KL

Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site

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

BioCatalogue: a universal catalogue of web services for the life sciences


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

Identification and classification of bcl genes and proteins of Bacillus cereus group organisms and their application in Bacillus anthracis detection and fingerprinting.

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

Integrating ELF4 into the circadian system through combined structural and functional studies.

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

Common design principles in the spliceosomal RNA helicase Brr2 and in the Hel308 DNA helicase.

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

SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes.

Zylicz-Stachula A, Bujnicki JM, Skowron PM

Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family.

Pawłowski M, Lasica AM, Jagusztyn-Krynicka EK, Bujnicki JM

AAN82231 protein from uropathogenic E. coli CFT073 is a close paralog of DsbB enzymes and does not belong to the DsbI family

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

YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA.

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

Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors

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

Medaka: a promising model animal for comparative population genomics.

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

Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system

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

The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein

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

Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.

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

MODOMICS: a database of RNA modification pathways. 2008 update

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

The mitotic kinesin-14 Ncd drives directional microtubule-microtubule sliding.

Majorek KA, Bujnicki JM

Modeling of Escherichia coli Endonuclease V structure in complex with DNA.


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

Mutational analysis and a structural model of methyl-directed restriction enzyme Mrr.

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

IAPs contain an evolutionarily conserved ubiquitin-binding domain that regulates NF-kappaB as well as cell survival and oncogenesis.

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

YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962

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

HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.

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

Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.

Pawlowski M, Gajda MJ, Matlak R, Bujnicki JM

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

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

YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.

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

The PMS2 subunit of human MutLalpha contains a metal ion binding domain of the iron-dependent repressor protein family.

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

Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.

Orlowski J, Bujnicki JM

Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.

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

The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).

Chua TK, Bujnicki JM, Tan TC, Huynh F, Patel BK, Sivaraman J

The structure of sucrose phosphate synthase from Halothermothrix orenii reveals its mechanism of action and binding mode.

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

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

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

EXOG, a novel paralog of Endonuclease G in higher eukaryotes.

Bhagwat AS, Carpenter MA, Bujnicki JM

Is AID a monomer in solution?

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

Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics.

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

The TbMTr1 spliced leader RNA cap 1 2'-O-ribose methyltransferase from Trypanosoma brucei acts with substrate specificity

Kaminska KH, Bujnicki JM

Bacteriophage Mu Mom protein responsible for DNA modification is a new member of the acyltransferase superfamily.

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

Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA.

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

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.

Vasu K, Saravanan M, Bujnicki JM, Nagaraja V

Structural integrity of the beta beta alpha-Metal finger motif is required for DNA binding and stable protein-DNA complex formation in R.KpnI.

Maravić Vlahovicek G, Cubrilo S, Tkaczuk KL, Bujnicki JM

Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm.


Chovancová E, Kosinski J, Bujnicki JM, Damborský J

Phylogenetic analysis of haloalkane dehalogenases.

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

Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily.

Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A

Identification of a single HNH active site in type IIS restriction endonuclease Eco31I

Koscinski L, Feder M, Bujnicki JM

Identification of a missing sequence and functionally important residues of 16S rRNA:m(1)A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics.

Kosinski J, Kubareva E, Bujnicki JM

A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.

Kudan EV, Brevnov MG, Subach OM, Rechkoblit OA, Buĭnitskiĭ IaM, Gromova ES

[Probing of contacts between EcoRII DNA methyltransferase and DNA using substrate analogs and molecular modeling].

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

Structure and evolutionary origin of Ca(2+)-dependent herring type II antifreeze protein.

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

Novel protein fold discovered in the PabI family of restriction enzymes.

Orlowski J, Boniecki M, Bujnicki JM

I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition

Ozanick SG, Bujnicki JM, Sem DS, Anderson JT

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

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

Structure of a multipartite protein-protein interaction domain in splicing factor prp8 and its link to retinitis pigmentosa.

Pietal MJ, Tuszynska I, Bujnicki JM

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.

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

Transcriptome profile of human colorectal adenomas.

Sasin JM, Godzik A, Bujnicki JM

SURF'S UP! - protein classification by surface comparisons

Schäfer P, Cymerman IA, Bujnicki JM, Meiss G

Human lysosomal DNase IIalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species.

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

Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC.

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

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

Zamudio JR, Mittra B, Foldynová-Trantírková S, Zeiner GM, Lukes J, Bujnicki JM, Sturm NR, Campbell DA

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


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

MODOMICS: a database of RNA modification pathways.

Bheemanaik S, Bujnicki JM, Nagaraja V, Rao DN

Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase.

Bujnicki JM

Protein-structure prediction by recombination of fragments.

Carpenter M, Divvela P, Pingoud V, Bujnicki J, Bhagwat AS

Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI.

Chiang PK, Bujnicki JM, Su X, Lanar DE

Malaria: therapy, genes and vaccines.

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

Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease

Dunin-Horkawicz S, Feder M, Bujnicki JM

Phylogenomic analysis of the GIY-YIG nuclease superfamily.

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

THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.

Godlewska R, Dzwonek A, Mikuła M, Ostrowski J, Pawłowski M, Bujnicki JM, Jagusztyn-Krynicka EK

Helicobacter pylori protein oxidation influences the colonization process.

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

Characterization of prmt7alpha and beta isozymes from Chinese hamster cells sensitive and resistant to topoisomerase II inhibitors.

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

Binding of the low-density lipoprotein by streptococcal collagen-like protein Scl1 of Streptococcus pyogenes.

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

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

Metz J, Wächter A, Schmidt B, Bujnicki JM, Schwappach B

The yeast Arr4p ATPase binds the chloride transporter Gef1p when copper is available in the cytosol.

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

Casein kinases phosphorylate multiple residues spanning the entire hnRNP K length.

Obarska A, Blundell A, Feder M, Vejsadová S, Sisáková E, Weiserová M, Bujnicki JM, Firman K

Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA.

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

The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase.

Samaranayake M, Bujnicki JM, Carpenter M, Bhagwat AS

Evaluation of molecular models for the affinity maturation of antibodies: roles of cytosine deamination by AID and DNA repair.

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

Curcumin induces caspase-3-dependent apoptotic pathway but inhibits DNA fragmentation factor 40/caspase-activated DNase endonuclease in human Jurkat cells.

Skowronek KJ, Kosinski J, Bujnicki JM

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis.

Tkaczuk KL, Obarska A, Bujnicki JM

Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis.

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

Complete cap 4 formation is not required for viability in Trypanosoma brucei.

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

Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.


Armalyte E, Bujnicki JM, Giedriene J, Gasiunas G, Kosiński J, Lubys A

Mva1269I: a monomeric type IIS restriction endonuclease from Micrococcus varians with two EcoRI- and FokI-like catalytic domains.

Bujnicki J.M.

Przewidywanie struktury bialek: Boltzmann i Darwin

Chmiel AA, Bujnicki JM, Skowronek KJ

A homology model of restriction endonuclease SfiI in complex with DNA

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

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.

Cymerman IA, Meiss G, Bujnicki JM

DNase II is a member of the phospholipase D superfamily.

Feder M, Bujnicki JM

Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.

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

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

Koliński A, Bujnicki JM

Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.

Kosinski J, Feder M, Bujnicki JM

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.

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

Analysis of the quaternary structure of the MutL C-terminal domain.

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

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

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

Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII

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

Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences

Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

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

Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.

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

Characterization 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.

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

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.

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

Molecular modeling of a psychrophilic β-galactosidase

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

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

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

Analysis of the quaternary structure of the MutL C-terminal domain.

Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B

Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.

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

Characterization 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.

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

Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.

Radlińska M, Piekarowicz A, Galimand M, Bujnicki JM

Cloning and preliminary characterization of a GATC-specific beta2-class DNA:m6A methyltransferase encoded by transposon Tn1549 from Enterococcus spp.


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

N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.

Bujnicki JM, Feder M, Ayres CL, Redman KL

Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.

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

Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.

Koudan EV, Bujnicki JM, Gromova ES

Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.

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

N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.

Bujnicki JM, Feder M, Ayres CL, Redman KL

Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.

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

Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA.

Koudan EV, Bujnicki JM, Gromova ES

Homology modeling of the CG-specific DNA methyltransferase SssI and its complexes with DNA and AdoHcy.

Maravić G, Bujnicki JM, Flögel M

Mutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'

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

Sterol methyltransferase: functional analysis of highly conserved residues by site-directed mutagenesis.

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

Cooperative binding of the hnRNP K three KH domains to mRNA targets.

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

Geometric analysis of cross-linkability for protein fold discrimination.

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

A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase

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

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

Sasin JM, Bujnicki JM

COLORADO3D, a web server for the visual analysis of protein structures.

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

Structural and functional characterization of mitochondrial EndoG, a sugar non-specific nuclease which plays an important role during apoptosis.

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

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.


Maravić G, Feder M, Pongor S, Flögel M, Bujnicki JM

Mutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'

Mouaikel J, Bujnicki JM, Tazi J, Bordonné R

Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase

Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Lüder G, Xu SY, Pingoud A

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

Sasin JM, Kurowski MA, Bujnicki JM

STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.

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

Experimental evidence for a beta beta alpha-Me-finger nuclease motif to represent the active site of the caspase-activated DNase.

Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE

Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.

Coker JA, Sheridan PP, Loveland-Curtze J, Gutshall KR, Auman AJ, Brenchley JE

Biochemical characterization of a beta-galactosidase with a low temperature optimum obtained from an Antarctic arthrobacter isolate.

Bujnicki JM

Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology

Bujnicki JM, Albert MA, Nelson DJ, Thurlow DL

Fold recognition, homology modeling, docking simulations, kinetics analysis and mutagenesis of ATP/CTP:tRNA nucleotidyltransferase from Methanococcus jannaschii.

Bujnicki JM, Prigge ST, Caridha D, Chiang PK

Structure, evolution, and inhibitor interaction of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum.

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

The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase.

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

Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures.

Feder M, Pas J, Wyrwicz LS, Bujnicki JM

Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases

Gordon RK, Ginalski K, Rudnicki WR, Rychlewski L, Pankaskie MC, Bujnicki JM, Chiang PK

Anti-HIV-1 activity of 3-deaza-adenosine analogs. Inhibition of S-adenosylhomocysteine hydrolase and nucleotide congeners.

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

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

Kurowski MA, Bhagwat AS, Papaj G, Bujnicki JM

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.

Kurowski MA, Bujnicki JM

GeneSilico protein structure prediction meta-server.

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

Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures.

Maravić G, Bujnicki JM, Feder M, Pongor S, Flögel M

Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions


Bujnicki JM

Sequence permutations in the molecular evolution of DNA methyltransferases

Bujnicki JM, Blumenthal RM, Rychlewski L

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

Bujnicki JM, Feder M, Radlinska M, Blumenthal RM

Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase

Bujnicki JM, Feder M, Rychlewski L, Fischer D

Errors in the D. radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools

Bujnicki JM, Leach RA, Debski J, Rychlewski L

Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family

Bujnicki JM, Rychlewski L

Fold-recognition analysis predicts that the Tag protein family shares a common domain with the helix-hairpin-helix DNA glycosylases

Bujnicki JM, Rychlewski L

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

Bujnicki JM, Rychlewski L

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

Bujnicki J, Rychlewski L, Fischer D

Fold-recognition detects an error in the Protein Data Bank

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

The hppA gene of Helicobacter pylori encodes the class C acid phosphatase precursor

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

Evolutionary relationship between different subgroups of restriction endonucleases.

Pintard L, Bujnicki JM, Lapeyre B, Bonnerot C

MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase

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

Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop

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

Streptococcal Scl1 and Scl2 proteins form collagen-like triple helices.

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

Angiogenesis inhibitors specific for methionine aminopeptidase 2 as drugs for malaria and leishmaniasis


Bujnicki JM

In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea

Bujnicki JM

Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons.

Bujnicki JM

A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide.

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

Structure prediction meta server

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

LiveBench-1: continuous benchmarking of protein structure prediction servers

Bujnicki JM, Elofsson A, Fischer D, Rychlewski L

LiveBench-2: large-scale automated evaluation of protein structure prediction servers.

Bujnicki JM, Feder M, Radlinska M, Rychlewski L

mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships

Bujnicki JM, Radlinska M

Cloning and characterization of M.LmoA118I, a novel DNA:m4C methyltransferase from the Listeria monocytogenes phage A118, a close homolog of M.NgoMXV

Bujnicki JM, Radlinska M, Rychlewski L

Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed

Bujnicki JM, Radlinska M, Zaleski P, Piekarowicz A

Cloning of the Haemophilus influenzae Dam methyltransferase and analysis of its relationship to the Dam methyltransferase encoded by the HP1 phage

Bujnicki JM, Rotkiewicz P, Kolinski A, Rychlewski L

Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics.

Bujnicki JM, Rychlewski L

Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases

Bujnicki JM, Rychlewski L

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

Bujnicki JM, Rychlewski L

Unusual evolutionary history of the tRNA splicing endonuclease EndA: relationship to the LAGLIDADG and PD-(D/E)XK deoxyribonucleases.

Bujnicki JM, Rychlewski L

Reassignment of specificities of two cap methyltransferase domains in the reovirus lambda 2 protein

Bujnicki JM, Rychlewski L

Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles.

Bujnicki JM, Rychlewski L

The herpesvirus alkaline exonuclease belongs to the restriction endonuclease PD-(D/E)XK superfamily: insight from molecular modeling and phylogenetic analysis.

Lundström J, Rychlewski L, Bujnicki J, Elofsson A

Pcons: a neural-network-based consensus predictor that improves fold recognition

Radlinska M, Bujnicki JM

Cloning of enterohemorrhagic Escherichia coli phage VT-2 dam methyltransferase

Radlinska M, Bujnicki JM

Site-directed mutagenesis defines the catalytic aspartate in the active site of the atypical DNA: m4C methyltransferase M.NgoMXV


Bujnicki JM

Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases.

Bujnicki JM

Sequence, structural, and evolutionary analysis of prokaryotic ribosomal protein L11 methyltransferases.

Bujnicki JM, Radlinska M, Rychlewski L

Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to betabetaalphaMe endonucleases

Bujnicki JM, Rychlewski L

Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs

Bujnicki JM, Rychlewski L

Prediction of a common fold for all four subunits of the yeast tRNA splicing endonuclease: implications for the evolution of the EndA/Sen family.