Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots. - Mateusz Sikora; Joanna I. Sulkowska; Marek Cieplak (PLoS Comput. Biol., 2009)

A Stevedore's Protein Knot. - Daniel Bölinger; Joanna I. Sulkowska; Hsiao-Ping Hsu; Leonid A. Mirny; Mehran Kardar; José N. Onuchic; Peter Virnau (PLoS Comput. Biol., 2010)

BSDB: the biomolecule stretching database. - Mateusz Sikora; Joanna I. Sulkowska; Bartlomiej S. Witkowski; Marek Cieplak (Nucleic Acids Res., 2011)

Pierced Lasso Bundles Are a New Class of Knot-like Motifs. - Ellinor Haglund; Joanna I. Sulkowska; Jeffrey K. Noel; Heiko Lammert; José N. Onuchic; Patricia A. Jennings (PLoS Comput. Biol., 2014)

KnotProt: a database of proteins with knots and slipknots. - Michal Jamróz 001; Wanda Niemyska; Eric J. Rawdon; Andrzej Stasiak; Kenneth C. Millett; Piotr Sulkowski; Joanna I. Sulkowska (Nucleic Acids Res., 2015)

LassoProt: server to analyze biopolymers with lassos. - Pawel Dabrowski-Tumanski; Wanda Niemyska; Pawel Pasznik; Joanna I. Sulkowska (Nucleic Acids Res., 2016)

PyLasso: a PyMOL plugin to identify lassos. - Aleksandra Maria Gierut; Wanda Niemyska; Pawel Dabrowski-Tumanski; Piotr Sulkowski; Joanna I. Sulkowska (Bioinform., 2017)

LinkProt: a database collecting information about biological links. - Pawel Dabrowski-Tumanski; Aleksandra I. Jarmolinska; Wanda Niemyska; Eric J. Rawdon; Kenneth C. Millett; Joanna I. Sulkowska (Nucleic Acids Res., 2017)

GapRepairer: a server to model a structural gap and validate it using topological analysis. - Aleksandra I. Jarmolinska; Michal Kadlof; Pawel Dabrowski-Tumanski; Joanna I. Sulkowska (Bioinform., 2018)

KnotGenome: a server to analyze entanglements of chromosomes. - Joanna I. Sulkowska; Szymon Niewieczerzal; Aleksandra I. Jarmolinska; Jonathan T. Siebert; Peter Virnau; Wanda Niemyska (Nucleic Acids Res., 2018)

The exclusive effects of chaperonin on the behavior of proteins with 52 knot. - Yani Zhao; Pawel Dabrowski-Tumanski; Szymon Niewieczerzal; Joanna I. Sulkowska (PLoS Comput. Biol., 2018)

PyLink: a PyMOL plugin to identify links. - Aleksandra Maria Gierut; Pawel Dabrowski-Tumanski; Wanda Niemyska; Kenneth C. Millett; Joanna I. Sulkowska (Bioinform., 2019)

DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings. - Aleksandra I. Jarmolinska; Qin Zhou; Joanna I. Sulkowska; Faruck Morcos (J. Chem. Inf. Model., 2019)

KnotProt 2.0: a database of proteins with knots and other entangled structures. - Pawel Dabrowski-Tumanski; Pawel Rubach; Dimos Goundaroulis; Julien Dorier; Piotr Sulkowski; Kenneth C. Millett; Eric J. Rawdon; Andrzej Stasiak; Joanna I. Sulkowska (Nucleic Acids Res., 2019)

Knot_pull - python package for biopolymer smoothing and knot detection. - Aleksandra I. Jarmolinska; Anna Gambin; Joanna I. Sulkowska (Bioinform., 2020)

Genus for biomolecules. - Pawel Rubach; Sebastian Zajac; Borys Jastrzebski; Joanna I. Sulkowska; Piotr Sulkowski (Nucleic Acids Res., 2020)

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites. - Agata P. Perlinska; Adam Stasiulewicz; Ewa K. Nawrocka; Krzysztof Kazimierczuk; Piotr Setny; Joanna I. Sulkowska (PLoS Comput. Biol., 2020)

Topoly: Python package to analyze topology of polymers. - Pawel Dabrowski-Tumanski; Pawel Rubach; Wanda Niemyska; Bartosz Ambrozy Gren; Joanna I. Sulkowska (Briefings 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)

AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. - Wanda Niemyska; Pawel Rubach; Bartosz Ambrozy Gren; Mai Lan Nguyen; Wojciech Garstka; Fernando Bruno da Silva; Eric J. Rawdon; Joanna I. Sulkowska (Nucleic Acids Res., 2022)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding. - Agata P. Perlinska; Adam Stasiulewicz; Mai Lan Nguyen; Karolina Swiderska; Mikolaj Zmudzinski; Alicja W. Maksymiuk; Marcin Drag; Joanna I. Sulkowska (PLoS Comput. Biol., 2022)

Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation. - Adam Stasiulewicz; Anna Lesniak; Magdalena Bujalska-Zadrozny; Tomasz Pawinski; Joanna I. Sulkowska (J. Chem. Inf. Model., 2023)

Knotted artifacts in predicted 3D RNA structures. - Bartosz Ambrozy Gren; Maciej Antczak; Tomasz Zok; Joanna I. Sulkowska; Marta Szachniuk (PLoS Comput. Biol., 2024)