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)

Structure prediction meta server. - Janusz M. Bujnicki; Arne Elofsson; Daniel Fischer 001; Leszek Rychlewski (Bioinform., 2001)

mRNA: guanine-N7 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)

Fold-recognition detects an error in the Protein Data Bank. - Janusz M. Bujnicki; Leszek Rychlewski; Daniel Fischer 001 (Bioinform., 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)

STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification. - Joanna M. Sasin; Michal A. Kurowski; Janusz M. Bujnicki (ISMB (Supplement of Bioinformatics), 2003)

Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures. - Michal A. Kurowski; Joanna M. Sasin; Marcin Feder; Janusz Debski; Janusz M. Bujnicki (BMC Bioinform., 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)

GeneSilico protein structure prediction meta-server. - Michal A. Kurowski; Janusz M. Bujnicki (Nucleic Acids Res., 2003)

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 (Pacific Symposium on Biocomputing, 2004)

COLORADO3D, a web server for the visual analysis of protein structures. - Joanna M. Sasin; Janusz M. Bujnicki (Nucleic Acids Res., 2004)

DNase II is a member of the phospholipase D superfamily. - Iwona A. Cymerman; Gregor Meiss; Janusz M. Bujnicki (Bioinform., 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)

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)

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)

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. - Michal J. Pietal; Irina Tuszynska; Janusz M. Bujnicki (Bioinform., 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)

MetaMQAP: A meta-server for the quality assessment of protein models. - Marcin Pawlowski 001; Michal J. Gajda; Ryszard Matlak; Janusz M. Bujnicki (BMC Bioinform., 2008)

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 001; Janusz M. Bujnicki; Robert Preissner (Algorithms, 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)

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)

ModeRNA builds RNA 3D Models from Template Structures. - Magdalena Musielak; Kristian Rother; Tomasz Puton; Janusz M. Bujnicki (ERCIM News, 2010)

RNA tertiary structure prediction with ModeRNA. - Magdalena Rother; Kristian Rother; Tomasz Puton; Janusz M. Bujnicki (Briefings 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)

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking. - Irina Tuszynska; Janusz M. Bujnicki (BMC Bioinform., 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)

A toolbox for developing bioinformatics software. - Kristian Rother; Wojciech Potrzebowski; Tomasz Puton; Magdalena Rother; Ewa Wywial; Janusz M. Bujnicki (Briefings 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)

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)

Molecular evolution of dihydrouridine synthases. - Joanna M. Kasprzak; Anna Czerwoniec; 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)

The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement. - Marcin Pawlowski 001; Janusz M. Bujnicki (BMC Bioinform., 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)

Intrinsic Disorder in the Human Spliceosomal Proteome. - Iga Korneta; Janusz M. Bujnicki (PLoS Comput. Biol., 2012)

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; et al. (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)

QA-RecombineIt: a server for quality assessment and recombination of protein models. - Marcin Pawlowski 001; Albert Bogdanowicz; Janusz M. Bujnicki (Nucleic Acids Res., 2013)

Bioinformatics and Computational Biology in Poland. - Janusz M. Bujnicki; Jerzy Tiuryn (PLoS Comput. Biol., 2013)

RNA Bricks - a database of RNA 3D motifs and their interactions. - Grzegorz Chojnowski; Tomasz Walen; Janusz M. Bujnicki (Nucleic Acids Res., 2014)

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)

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)

NPDock: a web server for protein-nucleic acid docking. - Irina Tuszynska; Marcin Magnus; Katarzyna Jonak; Wayne Dawson; Janusz M. Bujnicki (Nucleic Acids Res., 2015)

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)

RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. - Pietro Boccaletto; Marcin Magnus; Catarina Almeida 002; Adriana Zyla; Astha Astha; Radoslaw Pluta; Blazej Baginski; Elzbieta Jankowska; Stanislaw Dunin-Horkawicz; Tomasz K. Wirecki; Michal J. Boniecki; Filip Stefaniak; et al. (Nucleic Acids Res., 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)

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)

RNA 3D structure prediction guided by independent folding of homologous sequences. - Marcin Magnus; Kalli Kappel; Rhiju Das; Janusz M. Bujnicki (BMC Bioinform., 2019)

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)

DNAmoreDB, a database of DNAzymes. - Almudena Ponce-Salvatierra; Pietro Boccaletto; Janusz M. Bujnicki (Nucleic Acids Res., 2021)

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. - Filip Stefaniak; Janusz M. Bujnicki (PLoS Comput. Biol., 2021)

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; et al. (Nucleic Acids Res., 2022)

DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes. - Razieh Mohammadi-Arani; Fatemeh Javadi-Zarnaghi; Pietro Boccaletto; Janusz M. Bujnicki; Almudena Ponce-Salvatierra (Nucleic Acids Res., 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)

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., 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., 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., 2023)