Janusz M. Bujnicki

According to our database, Janusz M. Bujnicki authored at least 56 papers between 1999 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.

Grzegorz Chojnowski, Rafal Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki

Bioinform., September, 2023

Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA.

Natalia A Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak

Briefings Bioinform., July, 2023

NACDDB: Nucleic Acid Circular Dichroism Database.

Andrea Cappannini, Kevin Mosca, Sunandan Mukherjee, Seyed Naeim Moafinejad, Richard R. Sinden, Veronique Arluison, Janusz M. Bujnicki, Frank Wien

Nucleic Acids Res., January, 2023

2022

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

Natalia Szulc, Zuzanna Mackiewicz, Janusz M. Bujnicki, Filip Stefaniak

PLoS Comput. Biol., 2022

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

Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki, Almudena Ponce-Salvatierra

Nucleic Acids Res., 2022

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

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

Nucleic Acids Res., 2022

2021

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

Filip Stefaniak, Janusz M. Bujnicki

PLoS Comput. Biol., 2021

DNAmoreDB, a database of DNAzymes.

Almudena Ponce-Salvatierra, Pietro Boccaletto, Janusz M. Bujnicki

Nucleic Acids Res., 2021

2020

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

Tomasz K. Wirecki, Katarzyna Merdas, Agata Bernat, Michal J. Boniecki, Janusz M. Bujnicki, Filip Stefaniak

Nucleic Acids Res., 2020

2019

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

Marcin Magnus, Kalli Kappel, Rhiju Das, Janusz M. Bujnicki

BMC Bioinform., 2019

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

Martyna Nowacka, Pietro Boccaletto, Elzbieta Jankowska, Tomasz Jarzynka, Janusz M. Bujnicki, Stanislaw Dunin-Horkawicz

Database J. Biol. Databases Curation, 2019

2018

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

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

Nucleic Acids Res., 2018

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

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

Nucleic Acids Res., 2018

2016

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

Marcin Magnus, Michal J. Boniecki, Wayne Dawson, Janusz M. Bujnicki

Nucleic Acids Res., 2016

2015

NPDock: a web server for protein-nucleic acid docking.

Irina Tuszynska, Marcin Magnus, Katarzyna Jonak, Wayne Dawson, Janusz M. Bujnicki

Nucleic Acids Res., 2015

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

Magdalena A. Machnicka, Katarzyna H. Kaminska, Stanislaw Dunin-Horkawicz, Janusz M. Bujnicki

BMC Bioinform., 2015

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

Michal J. Pietal, Janusz M. Bujnicki, Lukasz Pawel Kozlowski

Bioinform., 2015

2014

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

Grzegorz Chojnowski, Tomasz Walen, Janusz M. Bujnicki

Nucleic Acids Res., 2014

2013

Bioinformatics and Computational Biology in Poland.

Janusz M. Bujnicki, Jerzy Tiuryn

PLoS Comput. Biol., 2013

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

Marcin Pawlowski, Albert Bogdanowicz, Janusz M. Bujnicki

Nucleic Acids Res., 2013

RNApathwaysDB - a database of RNA maturation and decay pathways.

Kaja Milanowska, Katarzyna Mikolajczak, Anna Lukasik, Marcin Skorupski, Zuzanna Balcer, Magdalena A. Machnicka, Martyna Nowacka, Kristian Rother, Janusz M. Bujnicki

Nucleic Acids Res., 2013

MODOMICS: a database of RNA modification pathways - 2013 update.

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

Nucleic Acids Res., 2013

2012

Intrinsic Disorder in the Human Spliceosomal Proteome.

Iga Korneta, Janusz M. Bujnicki

PLoS Comput. Biol., 2012

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

Michal J. Pietal, Natalia Szostak, Kristian Rother, Janusz M. Bujnicki

BMC Bioinform., 2012

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

Marcin Pawlowski, Janusz M. Bujnicki

BMC Bioinform., 2012

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

Lukasz Pawel Kozlowski, Janusz M. Bujnicki

BMC Bioinform., 2012

Molecular evolution of dihydrouridine synthases.

Joanna M. Kasprzak, Anna Czerwoniec, Janusz M. Bujnicki

BMC Bioinform., 2012

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

Anna Philips, Kaja Milanowska, Grzegorz Lach, Michal J. Boniecki, Kristian Rother, Janusz M. Bujnicki

Bioinform., 2012

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

Grzegorz Chojnowski, Janusz M. Bujnicki, Matthias Bochtler

Bioinform., 2012

A toolbox for developing bioinformatics software.

Kristian Rother, Wojciech Potrzebowski, Tomasz Puton, Magdalena Rother, Ewa Wywial, Janusz M. Bujnicki

Briefings Bioinform., 2012

2011

REPAIRtoire - a database of DNA repair pathways.

Kaja Milanowska, Joanna Krwawicz, Grzegorz Papaj, Jan Kosinski, Katarzyna Poleszak, Justyna Lesiak, Ewelina Osinska, Kristian Rother, Janusz M. Bujnicki

Nucleic Acids Res., 2011

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

Irina Tuszynska, Janusz M. Bujnicki

BMC Bioinform., 2011

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

Magdalena Rother, Kaja Milanowska, Tomasz Puton, Jaroslaw Jeleniewicz, Kristian Rother, Janusz M. Bujnicki

Bioinform., 2011

RNA tertiary structure prediction with ModeRNA.

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

Briefings Bioinform., 2011

2010

ModeRNA builds RNA 3D Models from Template Structures.

Magdalena Musielak, Kristian Rother, Tomasz Puton, Janusz M. Bujnicki

ERCIM News, 2010

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

Michal J. Gajda, Irina Tuszynska, Marta Kaczor, Anastasia Yu. Bakulina, Janusz M. Bujnicki

Bioinform., 2010

2009

MODOMICS: a database of RNA modification pathways, update 2008

Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, Kristian Rother

Nucleic Acids Res., 2009

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

Raphael André Bauer, Kristian Rother, Peter Moor, Knut Reinert, Thomas Steinke, Janusz M. Bujnicki, Robert Preissner

Algorithms, 2009

2008

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

Marcin Pawlowski, Michal J. Gajda, Ryszard Matlak, Janusz M. Bujnicki

BMC Bioinform., 2008

2007

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

Karolina L. Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M. Bujnicki

BMC Bioinform., 2007

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

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

Bioinform., 2007

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

Jerzy Orlowski, Michal J. Boniecki, Janusz M. Bujnicki

Bioinform., 2007

2006

MODOMICS: a database of RNA modification pathways.

Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, Janusz M. Bujnicki

Nucleic Acids Res., 2006

2005

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.

Jan Kosinski, Marcin Feder, Janusz M. Bujnicki

BMC Bioinform., 2005

DNase II is a member of the phospholipase D superfamily.

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

Bioinform., 2005

2004

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

Joanna M. Sasin, Janusz M. Bujnicki

Nucleic Acids Res., 2004

Geometric Analysis of Cross-Linkability for Protein Fold Discrimination.

Shobha Potluri, Aly Azeem Khan, A. Kuzminykh, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg

Proceedings of the Biocomputing 2004, 2004

2003

GeneSilico protein structure prediction meta-server.

Michal A. Kurowski, Janusz M. Bujnicki

Nucleic Acids Res., 2003

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

Krzysztof Ginalski, Jakub Pas, Lucjan Stanislaw Wyrwicz, Marcin von Grotthuss, Janusz M. Bujnicki, Leszek Rychlewski

Nucleic Acids Res., 2003

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

Michal A. Kurowski, Joanna M. Sasin, Marcin Feder, Janusz Debski, Janusz M. Bujnicki

BMC Bioinform., 2003

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

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

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2002

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.

Janusz M. Bujnicki, Leszek Rychlewski

BMC Bioinform., 2002

Fold-recognition detects an error in the Protein Data Bank.

Janusz M. Bujnicki, Leszek Rychlewski, Daniel Fischer

Bioinform., 2002

2001

mRNA: guanine-<i>N</i>7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships.

Janusz M. Bujnicki, Marcin Feder, Monika Radlinska, Leszek Rychlewski

BMC Bioinform., 2001

Structure prediction meta server.

Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski

Bioinform., 2001

1999

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

Silico Biol., 1999