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)

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. - Karolina L. Tkaczuk; Stanislaw Dunin-Horkawicz; Elzbieta Purta; Janusz M. Bujnicki (BMC Bioinform., 2007)

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)

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)

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)

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)

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)

DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences. - Jan Ludwiczak; Aleksander Winski; Krzysztof Szczepaniak; Vikram Alva; Stanislaw Dunin-Horkawicz (Bioinform., 2019)

Self-analysis of repeat proteins reveals evolutionarily conserved patterns. - Matthew Merski; Krzysztof Mlynarczyk; Jan Ludwiczak; Jakub Skrzeczkowski; Stanislaw Dunin-Horkawicz; Maria W. Górna (BMC Bioinform., 2020)

A library of coiled-coil domains: from regular bundles to peculiar twists. - Krzysztof Szczepaniak; Adriana Bukala; Antonio Marinho da Silva Neto; Jan Ludwiczak; Stanislaw Dunin-Horkawicz (Bioinform., 2021)

Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. - Vasilina Zayats; Agata P. Perlinska; Aleksandra I. Jarmolinska; Borys Jastrzebski; Stanislaw Dunin-Horkawicz; Joanna I. Sulkowska (PLoS Comput. Biol., 2021)

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. - Kamil Kaminski; Jan Ludwiczak; Maciej Jasinski; Adriana Bukala; Rafal Madaj; Krzysztof Szczepaniak; Stanislaw Dunin-Horkawicz (Briefings Bioinform., 2022)

localpdb - a Python package to manage protein structures and their annotations. - Jan Ludwiczak; Aleksander Winski; Stanislaw Dunin-Horkawicz (Bioinform., 2022)

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models. - Kamil Kaminski; Jan Ludwiczak; Kamil Pawlicki; Vikram Alva; Stanislaw Dunin-Horkawicz (Bioinform., 2023)