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)

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)

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)

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)

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)