Janusz M. Bujnicki

发表

Faculty Opinions recommendation of ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.

Janusz M. Bujnicki, Pritha Ghosh, 2017 .

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

Janusz M. Bujnicki, Marcin Pawlowski, Michal J. Gajda, 2008, BMC Bioinformatics.

Faculty Opinions recommendation of Fitting corrections to an RNA force field using experimental data.

Janusz M. Bujnicki, Pritha Ghosh, 2019 .

A toolbox for developing bioinformatics

Janusz M. Bujnicki, Wojciech Potrzebowski, Tomasz Puton, 2011 .

Faculty Opinions recommendation of A deep learning framework to predict binding preference of RNA constituents on protein surface.

Janusz M. Bujnicki, Pritha Ghosh, 2020 .

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

Janusz M. Bujnicki, Irina Tuszynska, J. Bujnicki, 2011, BMC Bioinformatics.

Bioinformatics and Computational Biology in Poland

Jerzy Tiuryn, Janusz M. Bujnicki, J. Bujnicki, 2013, PLoS Comput. Biol..

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

Leszek Rychlewski, Marcin Feder, Janusz M. Bujnicki, 2001, BMC Bioinformatics.

RNApathwaysDB—a database of RNA maturation and decay pathways

Kristian Rother, Janusz M. Bujnicki, Kaja Milanowska, 2012, Nucleic Acids Res..

Protein Fold-Recognition and Experimental Structure Determination

Leszek Rychlewski, Daniel Fischer, Janusz M. Bujnicki, 2004 .

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

Leszek Rychlewski, Janusz M. Bujnicki, J. Bujnicki, 2002, BMC Bioinformatics.

Molecular evolution of dihydrouridine synthases

Janusz M. Bujnicki, Joanna M. Kasprzak, Anna Czerwoniec, 2012, BMC Bioinformatics.

NPDock: a web server for protein–nucleic acid docking

Janusz M. Bujnicki, Irina Tuszynska, Katarzyna Jonak, 2015, Nucleic Acids Res..

Faculty Opinions recommendation of ShaKer: RNA SHAPE prediction using graph kernel.

Janusz M. Bujnicki, Pritha Ghosh, 2019 .

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

Janusz M. Bujnicki, Marcin Pawlowski, J. Bujnicki, 2012, BMC Bioinformatics.

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

Thomas Steinke, Kristian Rother, Knut Reinert, 2009, Algorithms.

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

Janusz M. Bujnicki, Marcin Pawlowski, Albert Bogdanowicz, 2013, Nucleic Acids Res..

MODOMICS: a database of RNA modification pathways. 2017 update

Janusz M. Bujnicki, Valérie de Crécy-Lagard, Robert Ross, 2017, Nucleic Acids Res..

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

Janusz M. Bujnicki, Irina Tuszynska, Michal J. Pietal, 2007, Bioinform..

Faculty Opinions recommendation of Going beyond base-pairs: topology-based characterization of base-multiplets in RNA.

Janusz M. Bujnicki, Pritha Ghosh, 2019 .

First Steps of Protein Structure Prediction

Janusz M. Bujnicki, Karolina A. Majorek, Łukasz P. Kozłowski, 2008 .

Faculty Opinions recommendation of Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.

Janusz M. Bujnicki, Pritha Ghosh, 2018 .

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

Janusz M. Bujnicki, Michal Boniecki, Marcin Magnus, 2016, Nucleic Acids Res..

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

Janusz M. Bujnicki, Martyna Nowacka, Stanislaw Dunin-Horkawicz, 2019, Database.

Prediction of protein structures, functions, and interactions

Janusz M. Bujnicki, J. Bujnicki, 2008 .

ModeRNA builds RNA 3D Models from Template Structures

Kristian Rother, Janusz M. Bujnicki, Tomasz Puton, 2010, ERCIM News.

REPAIRtoire—a database of DNA repair pathways

Kristian Rother, Jan Kosinski, Janusz M. Bujnicki, 2010, Nucleic Acids Res..

Geometric Analysis of Cross-Linkability for Protein Fold Discrimination

Chris Bailey-Kellogg, Janusz M. Bujnicki, Alan M. Friedman, 2003, Pacific Symposium on Biocomputing.

MODOMICS: a database of RNA modification pathways

Marcin Feder, Janusz M. Bujnicki, Michal J. Gajda, 2005, Nucleic Acids Res..

Template Based Prediction of Three‐Dimensional Protein Structures: Fold Recognition and Comparative Modeling

Jan Kosinski, Janusz M. Bujnicki, Joanna M. Kasprzak, 2008 .

Structure Prediction for Alternatively Spliced Proteins

Janusz M. Bujnicki, Lukasz P. Kozlowski, Jerzy Orlowski, 2012 .

F1000Prime recommendation of Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Janusz M. Bujnicki, Pritha Ghosh, 2019 .

QRNAS: software tool for refinement of nucleic acid structures

Janusz M. Bujnicki, Juliusz Stasiewicz, Sunandan Mukherjee, 2019, BMC Structural Biology.

A toolbox for developing bioinformatics software

Kristian Rother, Janusz M. Bujnicki, Wojciech Potrzebowski, 2012, Briefings Bioinform..

Computational Methods for Protein Structure Prediction and Fold Recognition

Marcin Feder, Janusz M. Bujnicki, Iwona A. Cymerman, 2008 .

Bioinformatics Applications Note Structural Bioinformatics Moderna Server: an Online Tool for Modeling Rna 3d Structures

Kristian Rother, Janusz M. Bujnicki, Tomasz Puton, 2022 .

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

Janusz M. Bujnicki, Grzegorz Chojnowski, Matthias Bochtler, 2012, Bioinform..

Structural bioinformatics Advance Access publication November 21, 2011

Kristian Rother, Janusz M. Bujnicki, Kaja Milanowska, 2011 .

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

Kristian Rother, Janusz M. Bujnicki, Michal J. Pietal, 2012, BMC Bioinformatics.

RNA tertiary structure prediction with ModeRNA

Kristian Rother, Janusz M. Bujnicki, Tomasz Puton, 2011, Briefings Bioinform..

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

Marcin Feder, Jan Kosinski, Janusz M. Bujnicki, 2005, BMC Bioinformatics.

Virtual screening strategies in drug design - methods and applications

Janusz M. Bujnicki, Xavier Lucas, Joanna M. Kasprzak, 2011 .

Intrinsic Disorder in the Human Spliceosomal Proteome

Janusz M. Bujnicki, Iga Korneta, J. Bujnicki, 2012, PLoS Comput. Biol..

The data from GeneSilico MetaServer for CASP10 (2012) targets

Janusz M. Bujnicki, Lukasz P. Kozlowski, 2017 .

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

Janusz M. Bujnicki, Stanislaw Dunin-Horkawicz, Elzbieta Purta, 2007, BMC Bioinformatics.

ORFeus: detection of distant homology using sequence profiles and predicted secondary structure

Marcin von Grotthuss, Jakub Pas, Leszek Rychlewski, 2003, Nucleic Acids Res..

FILTREST3D: discrimination of structural models using restraints from experimental data

Janusz M. Bujnicki, Michal J. Gajda, Irina Tuszynska, 2010, Bioinform..

GeneSilico protein structure prediction meta-server

Janusz M. Bujnicki, Michal A. Kurowski, J. Bujnicki, 2003, Nucleic Acids Res..

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

Janusz M. Bujnicki, Catarina Almeida, Michal Boniecki, 2017, Nucleic Acids Res..

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

Janusz M. Bujnicki, Magdalena A. Machnicka, Stanislaw Dunin-Horkawicz, 2015, BMC Bioinformatics.

AnnapuRNA: a scoring function for predicting RNA-small molecule interactions

Janusz M. Bujnicki, Filip Stefaniak, J. Bujnicki, 2020, bioRxiv.

Studying Biomolecular Interactions: A Hybrid Approach

Sean A. McKenna, Janusz M. Bujnicki, Manuel Koch, 2017 .

Fold-recognition detects an error in the Protein Data Bank

Leszek Rychlewski, Daniel Fischer, Janusz M. Bujnicki, 2002, Bioinform..

Computational modeling of RNA 3D structure based on experimental data

Janusz M. Bujnicki, Pritha Ghosh, Sunandan Mukherjee, 2019, Bioscience reports.

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

Tomasz Walen, Janusz M. Bujnicki, Grzegorz Chojnowski, 2013, Nucleic Acids Res..

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

Janusz M. Bujnicki, Michal Boniecki, Jerzy Orlowski, 2007, Bioinform..

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

Janusz M. Bujnicki, Lukasz P. Kozlowski, J. Bujnicki, 2012, BMC Bioinformatics.

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

Janusz M. Bujnicki, Marcin Magnus, Kalli Kappel, 2019, BMC Bioinformatics.

Analytics of Protein‐DNA Interactions. By Harald Seitz (ed.)

Janusz M. Bujnicki, 2007 .

Faculty of 1000 evaluation for RNA structural dynamics as captured by molecular simulations: A comprehensive overview.

Janusz M. Bujnicki, Pritha Ghosh, 2018 .

Comparison of protein structures reveals monophyletic origin of AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation

Janusz M. Bujnicki, J. Bujnicki, 1999, Silico Biol..

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

Janusz M. Bujnicki, Michal A. Kurowski, Joanna M. Sasin, 2003, ISMB.

DNase II is a member of the phospholipase D superfamily

Janusz M. Bujnicki, Iwona A. Cymerman, Gregor Meiss, 2005, Bioinform..

Template-Based and Template-Free Modeling of RNA 3D Structure: Inspirations from Protein Structure Modeling

Janusz M. Bujnicki, Tomasz Puton, Michal Boniecki, 2012 .

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

Janusz M. Bujnicki, Michal J. Pietal, Lukasz P. Kozlowski, 2015, Bioinform..

Prediction of Protein Function from Theoretical Models

Daniel J. Rigden, Janusz M. Bujnicki, Iwona A. Cymerman, 2009 .

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

Marcin Feder, Janusz M. Bujnicki, Michal A. Kurowski, 2003, BMC Bioinformatics.

Structure prediction meta server

Arne Elofsson, Leszek Rychlewski, Daniel Fischer, 2001, Bioinform..

Protein Structure Prediction: Concepts and Applications. Anna Tramontano.

Janusz M. Bujnicki, 2006 .

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

Janusz M. Bujnicki, Joanna M. Sasin, J. Bujnicki, 2004, Nucleic Acids Res..

RNA fragment assembly with experimental restraints

Janusz M. Bujnicki, Marcin Magnus, Grzegorz Chojnowski, 2021, bioRxiv.

DNAmoreDB, a database of DNAzymes

Janusz M. Bujnicki, Pietro Boccaletto, Almudena Ponce-Salvatierra, 2020, Nucleic Acids Res..

Computational Modeling Methods for 3D Structure Prediction of Ribozymes

Janusz M. Bujnicki, Pritha Ghosh, Filip Stefaniak, 2021, Ribozymes.

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

Janusz M. Bujnicki, Filip Stefaniak, J. Bujnicki, 2021, PLoS Comput. Biol..

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

Janusz M. Bujnicki, Anna Muszewska, Stanislaw Dunin-Horkawicz, 2014, Nucleic acids research.

Phylogeny of the Restriction Endonuclease-Like Superfamily Inferred from Comparison of Protein Structures

Janusz M. Bujnicki, J. Bujnicki, 2000, Journal of Molecular Evolution.

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

Marcin Feder, Janusz M. Bujnicki, Kent L. Redman, 2004, Nucleic acids research.

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

Janusz M. Bujnicki, Elzbieta Purta, Karolina L. Tkaczuk, 2007, Nucleic acids research.

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

Alfred Pingoud, Janusz M. Bujnicki, J. Bujnicki, 2003 .

MODOMICS: a database of RNA modification pathways, update 2008

Kristian Rother, Janusz M. Bujnicki, Joanna M. Kasprzak, 2009, Nucleic Acids Res..

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

Janusz M. Bujnicki, Irina Tuszynska, J. Bujnicki, 2012, Nucleic acids research.

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

Janusz M. Bujnicki, Monika Radlinska, J. Bujnicki, 2005, Nucleic acids research.

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

Janusz M. Bujnicki, Michal J. Gajda, Irina Tuszynska, 2006, Nucleic Acids Research.

Trm11p and Trm112p Are both Required for the Formation of 2-Methylguanosine at Position 10 in Yeast tRNA

Janusz M. Bujnicki, S. K. Purushothaman, Henri Grosjean, 2005, Molecular and Cellular Biology.

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

Janusz M. Bujnicki, Stéphane Aymerich, Ingrid Zegers, 2006, Nucleic acids research.

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

Luigi Cavallo, Janusz M. Bujnicki, Mohit Chawla, 2017, Nucleic acids research.

HsdR Subunit of the Type I Restriction-Modification Enzyme EcoR124I: Biophysical Characterisation and Structural Modelling

Janusz M. Bujnicki, Agnieszka Obarska-Kosinska, J. Bujnicki, 2008, Journal of molecular biology.

Corrigendum: ''RNAcentral : a hub of information for non-coding RNA sequences'' [Nucleic acids research, 47 (2019) D1, p. D221-D229]

Robert D. Finn, James R. Cole, Alex Bateman, 2019 .

Structure Prediction and Phylogenetic Analysis of a Functionally Diverse Family of Proteins Homologous to the MT-A70 Subunit of the Human mRNA:m6A Methyltransferase

Marcin Feder, Janusz M. Bujnicki, Monika Radlinska, 2002, Journal of Molecular Evolution.

Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life

Janusz M. Bujnicki, Irina Tuszynska, Marcus Fislage, 2012, Nucleic acids research.

RNAlyzer—novel approach for quality analysis of RNA structural models

Jacek Blazewicz, Marta Szachniuk, Maciej Antczak, 2013, Nucleic acids research.

‘Meta’Approaches to Protein Structure Prediction

Daniel Fischer, Janusz M. Bujnicki, 2008 .

Bioinformatics-Guided Identification and Experimental Characterization of Novel RNA Methyltransferas

Janusz M. Bujnicki, S. K. Purushothaman, Henri Grosjean, 2008 .

RNA and protein 3D structure modeling: similarities and differences

Kristian Rother, Janusz M. Bujnicki, Tomasz Puton, 2011, Journal of molecular modeling.

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

Janusz M. Bujnicki, J. Bujnicki, Jerzy Orlowski, 2008, Nucleic acids research.

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

Janusz M. Bujnicki, Seth J. Davis, Heiko Schoof, 2009, HFSP journal.

Structural bioinformatics of the human spliceosomal proteome

Janusz M. Bujnicki, Marcin Magnus, Iga Korneta, 2012, Nucleic acids research.

SUPPLEMENTARY FIGURES AND TABLES FOR : Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms 2 io 6 A 37 in tRNA

Janusz M. Bujnicki, Michal Boniecki, Anna Czerwoniec, 2007 .

Angiogenesis Inhibitors Specific for Methionine Aminopeptidase 2 as Drugs for Malaria and Leishmaniasis

Janusz M. Bujnicki, Diarmuid E. Nicholson, Dennis E. Kyle, 2002, Journal of Biomedical Science.

Bud23 Methylates G1575 of 18S rRNA and Is Required for Efficient Nuclear Export of Pre-40S Subunits

Janusz M. Bujnicki, Edward M. Marcotte, Zhihua Li, 2008, Molecular and Cellular Biology.

The Basics of Protein Sequence Analysis

Janusz M. Bujnicki, Kaja Milanowska, Katarzyna H. Kaminska, 2008 .