Joanna I. Sulkowska

24 papers Journal 24
YearRankTypeTitle / Venue / Authors
2024 J jnl
Knotted artifacts in predicted 3D RNA structures.
PLoS Comput. Biol.
Bartosz Ambrozy Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk
2023 J jnl
Identification of Novel CB2 Ligands through Virtual Screening and In Vitro Evaluation.
J. Chem. Inf. Model.
Adam Stasiulewicz, Anna Lesniak, Magdalena Bujalska-Zadrozny, Tomasz Pawinski, Joanna I. Sulkowska
2022 J jnl
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods.
Nucleic Acids Res.
Wanda Niemyska, Pawel Rubach, Bartosz Ambrozy Gren, Mai Lan Nguyen, Wojciech Garstka, Fernando Bruno da Silva, Eric J. Rawdon, Joanna I. Sulkowska
2022 J jnl
Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding.
PLoS Comput. Biol.
Agata P. Perlinska, Adam Stasiulewicz, Mai Lan Nguyen, Karolina Swiderska, Mikolaj Zmudzinski, Alicja W. Maksymiuk, Marcin Drag, Joanna I. Sulkowska
2022 J jnl
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res.
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, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2021 J jnl
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.
PLoS Comput. Biol.
Vasilina Zayats, Agata P. Perlinska, Aleksandra I. Jarmolinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I. Sulkowska
2021 J jnl
Topoly: Python package to analyze topology of polymers.
Briefings Bioinform.
Pawel Dabrowski-Tumanski, Pawel Rubach, Wanda Niemyska, Bartosz Ambrozy Gren, Joanna I. Sulkowska
2020 J jnl
Genus for biomolecules.
Nucleic Acids Res.
Pawel Rubach, Sebastian Zajac, Borys Jastrzebski, Joanna I. Sulkowska, Piotr Sulkowski
2020 J jnl
Knot_pull - python package for biopolymer smoothing and knot detection.
Bioinform.
Aleksandra I. Jarmolinska, Anna Gambin, Joanna I. Sulkowska
2020 J jnl
Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites.
PLoS Comput. Biol.
Agata P. Perlinska, Adam Stasiulewicz, Ewa K. Nawrocka, Krzysztof Kazimierczuk, Piotr Setny, Joanna I. Sulkowska
2019 J jnl
DCA-MOL: A PyMOL Plugin To Analyze Direct Evolutionary Couplings.
J. Chem. Inf. Model.
Aleksandra I. Jarmolinska, Qin Zhou, Joanna I. Sulkowska, Faruck Morcos
2019 J jnl
KnotProt 2.0: a database of proteins with knots and other entangled structures.
Nucleic Acids Res.
Pawel Dabrowski-Tumanski, Pawel Rubach, Dimos Goundaroulis, Julien Dorier, Piotr Sulkowski, Kenneth C. Millett, Eric J. Rawdon, Andrzej Stasiak, Joanna I. Sulkowska
2019 J jnl
PyLink: a PyMOL plugin to identify links.
Bioinform.
Aleksandra Maria Gierut, Pawel Dabrowski-Tumanski, Wanda Niemyska, Kenneth C. Millett, Joanna I. Sulkowska
2018 J jnl
GapRepairer: a server to model a structural gap and validate it using topological analysis.
Bioinform.
Aleksandra I. Jarmolinska, Michal Kadlof, Pawel Dabrowski-Tumanski, Joanna I. Sulkowska
2018 J jnl
KnotGenome: a server to analyze entanglements of chromosomes.
Nucleic Acids Res.
Joanna I. Sulkowska, Szymon Niewieczerzal, Aleksandra I. Jarmolinska, Jonathan T. Siebert, Peter Virnau, Wanda Niemyska
2018 J jnl
The exclusive effects of chaperonin on the behavior of proteins with 52 knot.
PLoS Comput. Biol.
Yani Zhao, Pawel Dabrowski-Tumanski, Szymon Niewieczerzal, Joanna I. Sulkowska
2017 J jnl
LinkProt: a database collecting information about biological links.
Nucleic Acids Res.
Pawel Dabrowski-Tumanski, Aleksandra I. Jarmolinska, Wanda Niemyska, Eric J. Rawdon, Kenneth C. Millett, Joanna I. Sulkowska
2017 J jnl
PyLasso: a PyMOL plugin to identify lassos.
Bioinform.
Aleksandra Maria Gierut, Wanda Niemyska, Pawel Dabrowski-Tumanski, Piotr Sulkowski, Joanna I. Sulkowska
2016 J jnl
LassoProt: server to analyze biopolymers with lassos.
Nucleic Acids Res.
Pawel Dabrowski-Tumanski, Wanda Niemyska, Pawel Pasznik, Joanna I. Sulkowska
2015 J jnl
KnotProt: a database of proteins with knots and slipknots.
Nucleic Acids Res.
Michal Jamróz, Wanda Niemyska, Eric J. Rawdon, Andrzej Stasiak, Kenneth C. Millett, Piotr Sulkowski, Joanna I. Sulkowska
2014 J jnl
Pierced Lasso Bundles Are a New Class of Knot-like Motifs.
PLoS Comput. Biol.
Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings
2011 J jnl
BSDB: the biomolecule stretching database.
Nucleic Acids Res.
Mateusz Sikora, Joanna I. Sulkowska, Bartlomiej S. Witkowski, Marek Cieplak
2010 J jnl
A Stevedore's Protein Knot.
PLoS Comput. Biol.
Daniel Bölinger, Joanna I. Sulkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau
2009 J jnl
Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots.
PLoS Comput. Biol.
Mateusz Sikora, Joanna I. Sulkowska, Marek Cieplak