D
Dzmitry Padhorny
Researcher at Stony Brook University
Publications - 25
Citations - 2382
Dzmitry Padhorny is an academic researcher from Stony Brook University. The author has contributed to research in topics: Medicine & Fourier transform. The author has an hindex of 9, co-authored 21 publications receiving 1372 citations. Previous affiliations of Dzmitry Padhorny include Boston University & Moscow Institute of Physics and Technology.
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Journal ArticleDOI
The ClusPro web server for protein-protein docking.
Dima Kozakov,David R. Hall,Bing Xia,Kathryn A. Porter,Dzmitry Padhorny,Christine Yueh,Dmitri Beglov,Sandor Vajda +7 more
TL;DR: This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results of the ClusPro server.
Journal ArticleDOI
Allostery in Its Many Disguises: From Theory to Applications
Shoshana J. Wodak,Emanuele Paci,Nikolay V. Dokholyan,Nikolay V. Dokholyan,Igor N. Berezovsky,Amnon Horovitz,Jing Li,Vincent J. Hilser,Ivet Bahar,John Karanicolas,Gerhard Stock,Peter Hamm,Roland H. Stote,Jerome Eberhardt,Yassmine Chebaro,Annick Dejaegere,Marco Cecchini,Jean-Pierre Changeux,Peter G. Bolhuis,Jocelyne Vreede,Pietro Faccioli,Simone Orioli,Riccardo Ravasio,Le Yan,Carolina Brito,Matthieu Wyart,Paraskevi Gkeka,Ivan Rivalta,Giulia Palermo,Giulia Palermo,J. Andrew McCammon,Joanna Panecka-Hofman,Rebecca C. Wade,Rebecca C. Wade,Antonella Di Pizio,Masha Y. Niv,Ruth Nussinov,Chung-Jung Tsai,Hyunbum Jang,Dzmitry Padhorny,Dima Kozakov,Tom McLeish +41 more
TL;DR: An overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems is provided.
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
Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2.
Ryan M. Hekman,Adam J. Hume,Raghuveera Kumar Goel,Kristine M. Abo,Kristine M. Abo,Jessie Huang,Jessie Huang,Benjamin C. Blum,Rhiannon B. Werder,Rhiannon B. Werder,Ellen L Suder,Indranil Paul,Sadhna Phanse,Ahmed Youssef,Konstantinos D. Alysandratos,Konstantinos D. Alysandratos,Dzmitry Padhorny,Sandeep Ojha,Alexandra Mora-Martin,Dmitry A. Kretov,Peter E.A. Ash,Mamta Verma,Jian Zhao,J. J. Patten,Carlos Villacorta-Martin,Dante Bolzan,Carlos Perea-Resa,Esther Bullitt,Anne Hinds,Andrew Tilston-Lunel,Xaralabos Varelas,Shaghayegh Farhangmehr,Ulrich Braunschweig,Julian H. Kwan,Mark E. McComb,Avik Basu,Mohsan Saeed,Valentina Perissi,Eric J. Burks,Matthew D. Layne,John H Connor,Robert A. Davey,Ji-Xin Cheng,Benjamin Wolozin,Benjamin J. Blencowe,Stefan Wuchty,Shawn M. Lyons,Dima Kozakov,Daniel Cifuentes,Michael D. Blower,Michael D. Blower,Darrell N. Kotton,Darrell N. Kotton,Andrew A. Wilson,Andrew A. Wilson,Elke Mühlberger,Andrew Emili +56 more
TL;DR: Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity.
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.