A
Agnieszka G. Lipska
Researcher at University of Gdańsk
Publications - 24
Citations - 377
Agnieszka G. Lipska is an academic researcher from University of Gdańsk. The author has contributed to research in topics: Computer science & Molecular dynamics. The author has an hindex of 7, co-authored 19 publications receiving 202 citations. Previous affiliations of Agnieszka G. Lipska include Cornell University & Spanish National Research Council.
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Journal ArticleDOI
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Marc F. Lensink,Guillaume Brysbaert,Nurul Nadzirin,Sameer Velankar,Raphael A. G. Chaleil,Tereza Gerguri,Paul A. Bates,Elodie Laine,Alessandra Carbone,Alessandra Carbone,Sergei Grudinin,Ren Kong,Ranran Liu,Xu Ximing,Hang Shi,Shan Chang,Miriam Eisenstein,Agnieszka S. Karczyńska,Cezary Czaplewski,Emilia A. Lubecka,Agnieszka G. Lipska,Paweł Krupa,Magdalena A. Mozolewska,Łukasz Golon,Sergey A. Samsonov,Adam Liwo,Adam Liwo,Silvia Crivelli,Guillaume Pagès,Mikhail Karasikov,Maria Kadukova,Maria Kadukova,Yumeng Yan,Sheng-You Huang,Mireia Rosell,Mireia Rosell,Luis A. Rodríguez-Lumbreras,Luis A. Rodríguez-Lumbreras,Miguel Romero-Durana,Lucía Díaz-Bueno,Juan Fernández-Recio,Juan Fernández-Recio,Charles Christoffer,Genki Terashi,Woong-Hee Shin,Tunde Aderinwale,Sai Raghavendra Maddhuri Venkata Subraman,Daisuke Kihara,Dima Kozakov,Sandor Vajda,Kathyn Porter,Dzmitry Padhorny,Israel Desta,Dmitri Beglov,Mikhail Ignatov,Sergey Kotelnikov,Sergey Kotelnikov,Iain H. Moal,David W. Ritchie,Isaure Chauvot de Beauchêne,Bernard Maigret,Marie-Dominique Devignes,Maria Elisa Ruiz Echartea,Didier Barradas-Bautista,Zhen Cao,Luigi Cavallo,Romina Oliva,Yue Cao,Yang Shen,Minkyung Baek,Taeyong Park,Hyeonuk Woo,Chaok Seok,M. Braitbard,Lirane Bitton,Dina Scheidman-Duhovny,Justas Dapkūnas,Kliment Olechnovič,Česlovas Venclovas,Petras J. Kundrotas,Saveliy Belkin,Devlina Chakravarty,Varsha D. Badal,Ilya A. Vakser,Thom Vreven,Sweta Vangaveti,Tyler M. Borrman,Zhiping Weng,Johnathan D. Guest,Ragul Gowthaman,Brian G. Pierce,Xianjin Xu,Rui Duan,Liming Qiu,Jie Hou,Benjamin Ryan Merideth,Zhiwei Ma,Jianlin Cheng,Xiaoqin Zou,Panos Koukos,Jorge Roel-Touris,Francesco Ambrosetti,Cunliang Geng,Jörg Schaarschmidt,Mikael Trellet,Adrien S. J. Melquiond,Li C. Xue,Brian Jiménez-García,Charlotte W. van Noort,Rodrigo V. Honorato,Alexandre M. J. J. Bonvin,Shoshana J. Wodak +111 more
TL;DR: CAPRI Round 46 indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.
Journal ArticleDOI
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
Marc F. Lensink,Guillaume Brysbaert,Théo Mauri,Nurul Nadzirin,Sameer Velankar,Raphael A. G. Chaleil,Tereza Clarence,Paul A. Bates,Ren Kong,Bin Liu,Guangbo Yang,Ming Liu,Hang Shi,Xufeng Lu,Shan Chang,Raj S. Roy,Farhan Quadir,Jian Liu,Jianlin Cheng,Anna Antoniak,Cezary Czaplewski,Artur Giełdoń,Mateusz Kogut,Agnieszka G. Lipska,Adam Liwo,Emilia A. Lubecka,Martyna Maszota-Zieleniak,Adam K. Sieradzan,Rafał Ślusarz,Patryk A. Wesołowski,Patryk A. Wesołowski,Karolina Zięba,Carlos A. Del Carpio Muñoz,Eiichiro Ichiishi,Ameya Harmalkar,Jeffrey J. Gray,Alexandre M. J. J. Bonvin,Francesco Ambrosetti,Rodrigo V. Honorato,Zuzana Jandova,Brian Jiménez-García,Panagiotis I. Koukos,Siri Camee van Keulen,Charlotte W. van Noort,Manon Réau,Jorge Roel-Touris,Sergei Kotelnikov,Dzmitry Padhorny,Kathryn A. Porter,Andrey Alekseenko,Andrey Alekseenko,Mikhail Ignatov,Israel Desta,Ryota Ashizawa,Zhuyezi Sun,Usman Ghani,Nasser Hashemi,Sandor Vajda,Dima Kozakov,Mireia Rosell,Mireia Rosell,Luis A. Rodríguez-Lumbreras,Luis A. Rodríguez-Lumbreras,Juan Fernández-Recio,Juan Fernández-Recio,Agnieszka S. Karczyńska,Sergei Grudinin,Yumeng Yan,Hao Li,Peicong Lin,Sheng-You Huang,Charles Christoffer,Genki Terashi,Jacob Verburgt,Daipayan Sarkar,Tunde Aderinwale,Xiao Wang,Daisuke Kihara,Tsukasa Nakamura,Yuya Hanazono,Ragul Gowthaman,Johnathan D. Guest,Rui Yin,Ghazaleh Taherzadeh,Brian G. Pierce,Didier Barradas-Bautista,Zhen Cao,Luigi Cavallo,Romina Oliva,Yuanfei Sun,Shaowen Zhu,Yang Shen,Taeyong Park,Hyeonuk Woo,Jinsol Yang,Sohee Kwon,Jonghun Won,Chaok Seok,Yasuomi Kiyota,Shinpei Kobayashi,Yoshiki Harada,Mayuko Takeda-Shitaka,Petras J. Kundrotas,Amar Singh,Ilya A. Vakser,Justas Dapkūnas,Kliment Olechnovič,Česlovas Venclovas,Rui Duan,Liming Qiu,Xianjin Xu,Shuang Zhang,Xiaoqin Zou,Shoshana J. Wodak +113 more
TL;DR: The results of the CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge, were reported in this paper, where the prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top ranking models.
Journal ArticleDOI
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Paweł Krupa,Paweł Krupa,Magdalena A. Mozolewska,Magdalena A. Mozolewska,Marta Wiśniewska,Marta Wiśniewska,Yanping Yin,Yi He,Adam K. Sieradzan,Adam K. Sieradzan,Robert Ganzynkowicz,Agnieszka G. Lipska,Agnieszka G. Lipska,Agnieszka S. Karczyńska,Magdalena J. Ślusarz,Rafał Ślusarz,Artur Giełdoń,Cezary Czaplewski,Dawid Jagieła,Bartłomiej Zaborowski,Harold A. Scheraga,Adam Liwo +21 more
TL;DR: With further improvements of the UNRES force field that are now underway, the physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes.
Journal ArticleDOI
A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation
Adam Liwo,Adam K. Sieradzan,Agnieszka G. Lipska,Cezary Czaplewski,InSuk Joung,Wioletta Żmudzińska,Anna Hałabis,Stanisław Ołdziej +7 more
TL;DR: The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins and reproduced the bimodal distribution of backbone-virtual-bond angles in the simulated structures.
Journal ArticleDOI
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
Adam Liwo,Cezary Czaplewski,Adam K. Sieradzan,Agnieszka G. Lipska,Sergey A. Samsonov,Rajesh K. Murarka +5 more
TL;DR: In this article, the physical basis of coarse-grained molecular dynamics, the coarsegrained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications are discussed.