Janusz M. Bujnicki

57 papers Misc 1Journal 55Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders.
Briefings Bioinform.
Dávid Bajusz, Anita Rácz, Janusz M. Bujnicki, Filip Stefaniak
2023 J jnl
NACDDB: Nucleic Acid Circular Dichroism Database.
Nucleic Acids Res.
Andrea Cappannini, Kevin Mosca, Sunandan Mukherjee, Seyed Naeim Moafinejad, Richard R. Sinden, Veronique Arluison, Janusz M. Bujnicki, Frank Wien
2023 J jnl
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.
Bioinform.
Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki
2023 J jnl
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA.
Briefings Bioinform.
Natalia A Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak
2022 J jnl
DNAzymeBuilder, a web application for
Nucleic Acids Res.
Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki, Almudena Ponce-Salvatierra
2022 J jnl
MODOMICS: a database of RNA modification pathways. 2021 update.
Nucleic Acids Res.
Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elzbieta Purta, Malgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gülben Avsar, Antonia Romitelli, Pinar Pir, Erik Dassi, Silvestro G. Conticello, Francesc Aguiló, Janusz M. Bujnicki
2022 J jnl
fingeRNAt - A novel tool for high-throughput analysis of nucleic acid-ligand interactions.
PLoS Comput. Biol.
Natalia A Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak
2021 J jnl
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses.
PLoS Comput. Biol.
Filip Stefaniak, Janusz M. Bujnicki
2021 J jnl
DNAmoreDB, a database of DNAzymes.
Nucleic Acids Res.
Almudena Ponce-Salvatierra, Pietro Boccaletto, Janusz M. Bujnicki
2020 J jnl
RNAProbe: a web server for normalization and analysis of RNA structure probing data.
Nucleic Acids Res.
Tomasz K. Wirecki, Katarzyna Merdas, Agata Bernat, Michal J. Boniecki, Janusz M. Bujnicki, Filip Stefaniak
2019 J jnl
RNA 3D structure prediction guided by independent folding of homologous sequences.
BMC Bioinform.
Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki
2019 J jnl
RRMdb - an evolutionary-oriented database of RNA recognition motif sequences.
Database J. Biol. Databases Curation
Martyna Nowacka, Pietro Boccaletto, Elzbieta Jankowska, Tomasz Jarzynka, Janusz M. Bujnicki, Stanislaw Dunin-Horkawicz
2018 J jnl
MODOMICS: a database of RNA modification pathways. 2017 update.
Nucleic Acids Res.
Pietro Boccaletto, Magdalena A. Machnicka, Elzbieta Purta, Pawel Piatkowski, Blazej Baginski, Tomasz K. Wirecki, Valérie de Crécy-Lagard, Robert Ross, Patrick A. Limbach, Annika Kotter, Mark Helm, Janusz M. Bujnicki
2018 J jnl
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.
Nucleic Acids Res.
Pietro Boccaletto, Marcin Magnus, Catarina Almeida, Adriana Zyla, Astha Astha, Radoslaw Pluta, Blazej Baginski, Elzbieta Jankowska, Stanislaw Dunin-Horkawicz, Tomasz K. Wirecki, Michal J. Boniecki, Filip Stefaniak, Janusz M. Bujnicki
2016 J jnl
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.
Nucleic Acids Res.
Marcin Magnus, Michal J. Boniecki, Wayne Dawson, Janusz M. Bujnicki
2015 J jnl
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.
Bioinform.
Michal J. Pietal, Janusz M. Bujnicki, Lukasz Pawel Kozlowski
2015 J jnl
NPDock: a web server for protein-nucleic acid docking.
Nucleic Acids Res.
Irina Tuszynska, Marcin Magnus, Katarzyna Jonak, Wayne Dawson, Janusz M. Bujnicki
2015 J jnl
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
BMC Bioinform.
Magdalena A. Machnicka, Katarzyna H. Kaminska, Stanislaw Dunin-Horkawicz, Janusz M. Bujnicki
2014 J jnl
RNA Bricks - a database of RNA 3D motifs and their interactions.
Nucleic Acids Res.
Grzegorz Chojnowski, Tomasz Walen, Janusz M. Bujnicki
2013 J jnl
Bioinformatics and Computational Biology in Poland.
PLoS Comput. Biol.
Janusz M. Bujnicki, Jerzy Tiuryn
2013 J jnl
MODOMICS: a database of RNA modification pathways - 2013 update.
Nucleic Acids Res.
Magdalena A. Machnicka, Kaja Milanowska, Okan Osman Oglou, Elzbieta Purta, Malgorzata Kurkowska, Anna Olchowik, Witold Januszewski, Sebastian Kalinowski, Stanislaw Dunin-Horkawicz, Kristian Rother, Mark Helm, Janusz M. Bujnicki, Henri Grosjean
2013 J jnl
QA-RecombineIt: a server for quality assessment and recombination of protein models.
Nucleic Acids Res.
Marcin Pawlowski, Albert Bogdanowicz, Janusz M. Bujnicki
2013 J jnl
RNApathwaysDB - a database of RNA maturation and decay pathways.
Nucleic Acids Res.
Kaja Milanowska, Katarzyna Mikolajczak, Anna Lukasik, Marcin Skorupski, Zuzanna Balcer, Magdalena A. Machnicka, Martyna Nowacka, Kristian Rother, Janusz M. Bujnicki
2012 J jnl
A toolbox for developing bioinformatics software.
Briefings Bioinform.
Kristian Rother, Wojciech Potrzebowski, Tomasz Puton, Magdalena Rother, Ewa Wywial, Janusz M. Bujnicki
2012 J jnl
Intrinsic Disorder in the Human Spliceosomal Proteome.
PLoS Comput. Biol.
Iga Korneta, Janusz M. Bujnicki
2012 J jnl
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins.
BMC Bioinform.
Lukasz Pawel Kozlowski, Janusz M. Bujnicki
2012 J jnl
MetalionRNA: computational predictor of metal-binding sites in RNA structures.
Bioinform.
Anna Philips, Kaja Milanowska, Grzegorz Lach, Michal J. Boniecki, Kristian Rother, Janusz M. Bujnicki
2012 J jnl
Molecular evolution of dihydrouridine synthases.
BMC Bioinform.
Joanna M. Kasprzak, Anna Czerwoniec, Janusz M. Bujnicki
2012 J jnl
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes.
Bioinform.
Grzegorz Chojnowski, Janusz M. Bujnicki, Matthias Bochtler
2012 J jnl
RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures.
BMC Bioinform.
Michal J. Pietal, Natalia Szostak, Kristian Rother, Janusz M. Bujnicki
2012 J jnl
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement.
BMC Bioinform.
Marcin Pawlowski, Janusz M. Bujnicki
2011 J jnl
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking.
BMC Bioinform.
Irina Tuszynska, Janusz M. Bujnicki
2011 J jnl
ModeRNA server: an online tool for modeling RNA 3D structures.
Bioinform.
Magdalena Rother, Kaja Milanowska, Tomasz Puton, Jaroslaw Jeleniewicz, Kristian Rother, Janusz M. Bujnicki
2011 J jnl
REPAIRtoire - a database of DNA repair pathways.
Nucleic Acids Res.
Kaja Milanowska, Joanna Krwawicz, Grzegorz Papaj, Jan Kosinski, Katarzyna Poleszak, Justyna Lesiak, Ewelina Osinska, Kristian Rother, Janusz M. Bujnicki
2011 J jnl
RNA tertiary structure prediction with ModeRNA.
Briefings Bioinform.
Magdalena Rother, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki
2010 J jnl
FILTREST3D: discrimination of structural models using restraints from experimental data.
Bioinform.
Michal J. Gajda, Irina Tuszynska, Marta Kaczor, Anastasia Yu. Bakulina, Janusz M. Bujnicki
2010 J jnl
ModeRNA builds RNA 3D Models from Template Structures.
ERCIM News
Magdalena Musielak, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki
2009 J jnl
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors.
Algorithms
Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner
2009 J jnl
MODOMICS: a database of RNA modification pathways, update 2008
Nucleic Acids Res.
Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, Kristian Rother
2008 J jnl
MetaMQAP: A meta-server for the quality assessment of protein models.
BMC Bioinform.
Marcin Pawlowski, Michal J. Gajda, Ryszard Matlak, Janusz M. Bujnicki
2007 J jnl
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.
Bioinform.
Jerzy Orlowski, Michal J. Boniecki, Janusz M. Bujnicki
2007 J jnl
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure.
Bioinform.
Michal J. Pietal, Irina Tuszynska, Janusz M. Bujnicki
2007 J jnl
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
BMC Bioinform.
Karolina L. Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M. Bujnicki
2006 J jnl
MODOMICS: a database of RNA modification pathways.
Nucleic Acids Res.
Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, Janusz M. Bujnicki
2005 J jnl
DNase II is a member of the phospholipase D superfamily.
Bioinform.
Iwona A. Cymerman, Gregor Meiss, Janusz M. Bujnicki
2005 J jnl
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
BMC Bioinform.
Jan Kosinski, Marcin Feder, Janusz M. Bujnicki
2004 J jnl
COLORADO3D, a web server for the visual analysis of protein structures.
Nucleic Acids Res.
Joanna M. Sasin, Janusz M. Bujnicki
2004 Misc conf
Geometric Analysis of Cross-Linkability for Protein Fold Discrimination.
Pacific Symposium on Biocomputing
Shobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg
2003 J jnl
Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of
BMC Bioinform.
Michal A. Kurowski, Joanna M. Sasin, Marcin Feder, Janusz Debski, Janusz M. Bujnicki
2003 J jnl
GeneSilico protein structure prediction meta-server.
Nucleic Acids Res.
Michal A. Kurowski, Janusz M. Bujnicki
2003 J jnl
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure.
Nucleic Acids Res.
Krzysztof Ginalski, Jakub Pas, Lucjan Stanislaw Wyrwicz, Marcin von Grotthuss, Janusz M. Bujnicki, Leszek Rychlewski
2003 — conf
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.
ISMB (Supplement of Bioinformatics)
Joanna M. Sasin, Michal A. Kurowski, Janusz M. Bujnicki
2002 J jnl
Fold-recognition detects an error in the Protein Data Bank.
Bioinform.
Janusz M. Bujnicki, Leszek Rychlewski, Daniel Fischer
2002 J jnl
RNA: (guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited - bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
BMC Bioinform.
Janusz M. Bujnicki, Leszek Rychlewski
2001 J jnl
Structure prediction meta server.
Bioinform.
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
2001 J jnl
mRNA: guanine-
BMC Bioinform.
Janusz M. Bujnicki, Marcin Feder, Monika Radlinska, Leszek Rychlewski
1999 J jnl
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.
Silico Biol.
Janusz M. Bujnicki