Janusz M. Bujnicki

Publication Activity (10 Years)

Years Active: 1999-2023
Publications (10 Years): 14

Top Topics

Scoring Function

Structural Information

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Andrea Cappannini, Kevin Mosca, Sunandan Mukherjee, Seyed Naeim Moafinejad, Richard R. Sinden, Veronique Arluison, Janusz M. Bujnicki, Frank Wien
NACDDB: Nucleic Acid Circular Dichroism Database. Nucleic Acids Res. 51 (D1) (2023)
Natalia A Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA. Briefings Bioinform. 24 (4) (2023)
Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints. Bioinform. 39 (9) (2023)
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
MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 50 (D1) (2022)
Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki, Almudena Ponce-Salvatierra
generation of RNA/DNA-cleaving deoxyribozymes. Nucleic Acids Res. 50 (W1) (2022)
Natalia Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak
fingeRNAt - A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLoS Comput. Biol. 18 (6) (2022)
Almudena Ponce-Salvatierra, Pietro Boccaletto, Janusz M. Bujnicki
DNAmoreDB, a database of DNAzymes. Nucleic Acids Res. 49 (Database-Issue) (2021)
Filip Stefaniak, Janusz M. Bujnicki
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. PLoS Comput. Biol. 17 (2) (2021)
Tomasz K. Wirecki, Katarzyna Merdas, Agata Bernat, Michal J. Boniecki, Janusz M. Bujnicki, Filip Stefaniak
RNAProbe: a web server for normalization and analysis of RNA structure probing data. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki
RNA 3D structure prediction guided by independent folding of homologous sequences. BMC Bioinform. 20 (1) (2019)
Martyna Nowacka, Pietro Boccaletto, Elzbieta Jankowska, Tomasz Jarzynka, Janusz M. Bujnicki, Stanislaw Dunin-Horkawicz
RRMdb - an evolutionary-oriented database of RNA recognition motif sequences. Database J. Biol. Databases Curation 2019 (2019)
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
MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 46 (Database-Issue) (2018)
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
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. Nucleic Acids Res. 46 (Database-Issue) (2018)
Marcin Magnus, Michal J. Boniecki, Wayne Dawson, Janusz M. Bujnicki
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Magdalena A. Machnicka, Katarzyna H. Kaminska, Stanislaw Dunin-Horkawicz, Janusz M. Bujnicki
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. BMC Bioinform. 16 (2015)
Irina Tuszynska, Marcin Magnus, Katarzyna Jonak, Wayne Dawson, Janusz M. Bujnicki
NPDock: a web server for protein-nucleic acid docking. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Michal J. Pietal, Janusz M. Bujnicki, Lukasz P. Kozlowski
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. Bioinform. 31 (21) (2015)
Grzegorz Chojnowski, Tomasz Walen, Janusz M. Bujnicki
RNA Bricks - a database of RNA 3D motifs and their interactions. Nucleic Acids Res. 42 (Database-Issue) (2014)
Kaja Milanowska, Katarzyna Mikolajczak, Anna Lukasik, Marcin Skorupski, Zuzanna Balcer, Magdalena A. Machnicka, Martyna Nowacka, Kristian Rother, Janusz M. Bujnicki
RNApathwaysDB - a database of RNA maturation and decay pathways. Nucleic Acids Res. 41 (Database-Issue) (2013)
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
MODOMICS: a database of RNA modification pathways - 2013 update. Nucleic Acids Res. 41 (Database-Issue) (2013)
Janusz M. Bujnicki, Jerzy Tiuryn
Bioinformatics and Computational Biology in Poland. PLoS Comput. Biol. 9 (5) (2013)
Marcin Pawlowski, Albert Bogdanowicz, Janusz M. Bujnicki
QA-RecombineIt: a server for quality assessment and recombination of protein models. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Joanna M. Kasprzak, Anna Czerwoniec, Janusz M. Bujnicki
Molecular evolution of dihydrouridine synthases. BMC Bioinform. 13 (2012)
Marcin Pawlowski, Janusz M. Bujnicki
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement. BMC Bioinform. 13 (2012)
Iga Korneta, Janusz M. Bujnicki
Intrinsic Disorder in the Human Spliceosomal Proteome. PLoS Comput. Biol. 8 (8) (2012)
Kristian Rother, Wojciech Potrzebowski, Tomasz Puton, Magdalena Rother, Ewa Wywial, Janusz M. Bujnicki
A toolbox for developing bioinformatics software. Briefings Bioinform. 13 (2) (2012)
Michal J. Pietal, Natalia Szostak, Kristian Rother, Janusz M. Bujnicki
RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. BMC Bioinform. 13 (2012)
Anna Philips, Kaja Milanowska, Grzegorz Lach, Michal J. Boniecki, Kristian Rother, Janusz M. Bujnicki
MetalionRNA: computational predictor of metal-binding sites in RNA structures. Bioinform. 28 (2) (2012)
Grzegorz Chojnowski, Janusz M. Bujnicki, Matthias Bochtler
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes. Bioinform. 28 (6) (2012)
Lukasz P. Kozlowski, Janusz M. Bujnicki
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinform. 13 (2012)
Irina Tuszynska, Janusz M. Bujnicki
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking. BMC Bioinform. 12 (2011)
Magdalena Rother, Kaja Milanowska, Tomasz Puton, Jaroslaw Jeleniewicz, Kristian Rother, Janusz M. Bujnicki
ModeRNA server: an online tool for modeling RNA 3D structures. Bioinform. 27 (17) (2011)
Magdalena Rother, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki
RNA tertiary structure prediction with ModeRNA. Briefings Bioinform. 12 (6) (2011)
Kaja Milanowska, Joanna Krwawicz, Grzegorz Papaj, Jan Kosinski, Katarzyna Poleszak, Justyna Lesiak, Ewelina Osinska, Kristian Rother, Janusz M. Bujnicki
REPAIRtoire - a database of DNA repair pathways. Nucleic Acids Res. 39 (Database-Issue) (2011)
Magdalena Musielak, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki
ModeRNA builds RNA 3D Models from Template Structures. ERCIM News 2010 (82) (2010)
Michal J. Gajda, Irina Tuszynska, Marta Kaczor, Anastasia Yu. Bakulina, Janusz M. Bujnicki
FILTREST3D: discrimination of structural models using restraints from experimental data. Bioinform. 26 (23) (2010)
Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner
Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms 2 (2) (2009)
Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, Kristian Rother
MODOMICS: a database of RNA modification pathways, update 2008 Nucleic Acids Res. 37 (Database-Issue) (2009)
Marcin Pawlowski, Michal J. Gajda, Ryszard Matlak, Janusz M. Bujnicki
MetaMQAP: A meta-server for the quality assessment of protein models. BMC Bioinform. 9 (2008)
Karolina L. Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M. Bujnicki
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinform. 8 (2007)
Michal J. Pietal, Irina Tuszynska, Janusz M. Bujnicki
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. Bioinform. 23 (11) (2007)
Jerzy Orlowski, Michal J. Boniecki, Janusz M. Bujnicki
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition. Bioinform. 23 (5) (2007)
Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, Janusz M. Bujnicki
MODOMICS: a database of RNA modification pathways. Nucleic Acids Res. 34 (Database-Issue) (2006)
Iwona A. Cymerman, Gregor Meiss, Janusz M. Bujnicki
DNase II is a member of the phospholipase D superfamily. Bioinform. 21 (21) (2005)
Jan Kosinski, Marcin Feder, Janusz M. Bujnicki
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. 6 (2005)
Joanna M. Sasin, Janusz M. Bujnicki
COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Shobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg
Geometric Analysis of Cross-Linkability for Protein Fold Discrimination. Pacific Symposium on Biocomputing (2004)
Krzysztof Ginalski, Jakub Pas, Lucjan Stanislaw Wyrwicz, Marcin von Grotthuss, Janusz M. Bujnicki, Leszek Rychlewski
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res. 31 (13) (2003)
Michal A. Kurowski, Janusz M. Bujnicki
GeneSilico protein structure prediction meta-server. Nucleic Acids Res. 31 (13) (2003)
Joanna M. Sasin, Michal A. Kurowski, Janusz M. Bujnicki
STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification. ISMB (Supplement of Bioinformatics) (2003)
Michal A. Kurowski, Joanna M. Sasin, Marcin Feder, Janusz Debski, Janusz M. Bujnicki
-adenosylmethionine to three crystal structures. BMC Bioinform. 4 (2003)
Janusz M. Bujnicki, Leszek Rychlewski, Daniel Fischer
Fold-recognition detects an error in the Protein Data Bank. Bioinform. 18 (10) (2002)
Janusz M. Bujnicki, Leszek Rychlewski
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. 3 (2002)
Janusz M. Bujnicki, Marcin Feder, Monika Radlinska, Leszek Rychlewski
7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinform. 2 (2001)
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
Structure prediction meta server. Bioinform. 17 (8) (2001)
Janusz M. Bujnicki
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. 1 (4) (1999)