Joanna I. Sulkowska

According to our database, Joanna I. Sulkowska authored at least 24 papers between 2009 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Knotted artifacts in predicted 3D RNA structures.

Bartosz Ambrozy Gren, Maciej Antczak, Tomasz Zok, Joanna I. Sulkowska, Marta Szachniuk

PLoS Comput. Biol., 2024

2023

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., February, 2023

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., November, 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, 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

Nucleic Acids Res., 2022

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

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

Topoly: Python package to analyze topology of polymers.

Pawel Dabrowski-Tumanski, Pawel Rubach, Wanda Niemyska, Bartosz Ambrozy Gren, Joanna I. Sulkowska

Briefings Bioinform., 2021

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

Genus for biomolecules.

Pawel Rubach, Sebastian Zajac, Borys Jastrzebski, Joanna I. Sulkowska, Piotr Sulkowski

Nucleic Acids Res., 2020

Knot_pull - python package for biopolymer smoothing and knot detection.

Aleksandra I. Jarmolinska, Anna Gambin, Joanna I. Sulkowska

Bioinform., 2020

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

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

PyLink: a PyMOL plugin to identify links.

Aleksandra Maria Gierut, Pawel Dabrowski-Tumanski, Wanda Niemyska, Kenneth C. Millett, Joanna I. Sulkowska

Bioinform., 2019

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

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

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

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

PyLasso: a PyMOL plugin to identify lassos.

Aleksandra Maria Gierut, Wanda Niemyska, Pawel Dabrowski-Tumanski, Piotr Sulkowski, Joanna I. Sulkowska

Bioinform., 2017

2016

LassoProt: server to analyze biopolymers with lassos.

Pawel Dabrowski-Tumanski, Wanda Niemyska, Pawel Pasznik, Joanna I. Sulkowska

Nucleic Acids Res., 2016

2015

KnotProt: a database of proteins with knots and slipknots.

Michal Jamróz, Wanda Niemyska, Eric J. Rawdon, Andrzej Stasiak, Kenneth C. Millett, Piotr Sulkowski, Joanna I. Sulkowska

Nucleic Acids Res., 2015

2014

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

2011

BSDB: the biomolecule stretching database.

Mateusz Sikora, Joanna I. Sulkowska, Bartlomiej S. Witkowski, Marek Cieplak

Nucleic Acids Res., 2011

2010

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

2009

Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots.

Mateusz Sikora, Joanna I. Sulkowska, Marek Cieplak

PLoS Comput. Biol., 2009