An Algorithm for an Automatic NOE Pathways Analysis of 2D NMR Spectra of RNA Duplexes. - Ryszard W. Adamiak; Jacek Blazewicz; Piotr Formanowicz; Zofia Gdaniec; Marta Kasprzak; Mariusz Popenda; Marta Szachniuk (J. Comput. Biol., 2004)

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. - Mariusz Popenda; Marek Blazewicz; Marta Szachniuk; Ryszard W. Adamiak (Nucleic Acids Res., 2008)

An assignment walk through 3D NMR spectrum. - Marta Szachniuk; Mariusz Popenda; Ryszard W. Adamiak; Jacek Blazewicz (CIBCB, 2009)

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. - Mariusz Popenda; Marta Szachniuk; Marek Blazewicz; Szymon Wasik; Edmund K. Burke; Jacek Blazewicz; Ryszard W. Adamiak (BMC Bioinform., 2010)

MCQ4Structures to compute similarity of molecule structures. - Tomasz Zok; Mariusz Popenda; Marta Szachniuk (Central Eur. J. Oper. Res., 2014)

RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs. - Maciej Antczak; Tomasz Zok; Mariusz Popenda; Piotr Lukasiak; Ryszard W. Adamiak; Jacek Blazewicz; Marta Szachniuk (Nucleic Acids Res., 2014)

New in silico approach to assessing RNA secondary structures with non-canonical base pairs. - Agnieszka Rybarczyk; Natalia Szostak; Maciej Antczak; Tomasz Zok; Mariusz Popenda; Ryszard W. Adamiak; Jacek Blazewicz; Marta Szachniuk (BMC Bioinform., 2015)

RNAssess - a web server for quality assessment of RNA 3D structures. - Piotr Lukasiak; Maciej Antczak; Tomasz Ratajczak; Marta Szachniuk; Mariusz Popenda; Ryszard W. Adamiak; Jacek Blazewicz (Nucleic Acids Res., 2015)

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation. - Maciej Antczak; Mariusz Popenda; Tomasz Zok; Michal Zurkowski; Ryszard W. Adamiak; Marta Szachniuk (Bioinform., 2018)

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures. - Maciej Antczak; Tomasz Zok; Maciej Osowiecki; Mariusz Popenda; Ryszard W. Adamiak; Marta Szachniuk (BMC Bioinform., 2018)

RNApdbee 2.0: multifunctional tool for RNA structure annotation. - Tomasz Zok; Maciej Antczak; Michal Zurkowski; Mariusz Popenda; Jacek Blazewicz; Ryszard W. Adamiak; Marta Szachniuk (Nucleic Acids Res., 2018)

New models and algorithms for RNA pseudoknot order assignment. - Tomasz Zok; Jan Badura; Sylwester Swat; Kacper Figurski; Mariusz Popenda; Maciej Antczak (Int. J. Appl. Math. Comput. Sci., 2020)

Topology-based classification of tetrads and quadruplex structures. - Mariusz Popenda; Joanna Miskiewicz; Joanna Sarzynska; Tomasz Zok; Marta Szachniuk (Bioinform., 2020)

ElTetrado: a tool for identification and classification of tetrads and quadruplexes. - Tomasz Zok; Mariusz Popenda; Marta Szachniuk (BMC Bioinform., 2020)

RNAspider: a webserver to analyze entanglements in RNA 3D structures. - Kamil Luwanski; Vladyslav Hlushchenko; Mariusz Popenda; Tomasz Zok; Joanna Sarzynska; Daniil Martsich; Marta Szachniuk; Maciej Antczak (Nucleic Acids Res., 2022)