V
Vladimir Potapov
Researcher at New England Biolabs
Publications - 38
Citations - 1567
Vladimir Potapov is an academic researcher from New England Biolabs. The author has contributed to research in topics: DNA & Protein structure. The author has an hindex of 14, co-authored 33 publications receiving 1238 citations. Previous affiliations of Vladimir Potapov include Massachusetts Institute of Technology & Weizmann Institute of Science.
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Journal ArticleDOI
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.
TL;DR: Six different methods that were previously reported as being able to predict the change in protein stability (DeltaDeltaG) upon mutation are chosen: CC/PBSA, EGAD, FoldX, I-Mutant2.0, Rosetta and Hunter, and there is still room for improvement, which is crucial if the authors want forcefields to perform better in their various tasks.
Journal ArticleDOI
Examining Sources of Error in PCR by Single-Molecule Sequencing.
Vladimir Potapov,Jennifer L. Ong +1 more
TL;DR: A single-molecule sequencing assay was used to comprehensively catalog the different types of errors introduced during PCR, including polymerase misincorporation, structure-induced template-switching, PCR-mediated recombination and DNA damage.
Journal ArticleDOI
Community-wide assessment of protein-interface modeling suggests improvements to design methodology
Sarel J. Fleishman,Sarel J. Fleishman,Timothy A. Whitehead,Eva-Maria Strauch,Jacob E. Corn,Jacob E. Corn,Sanbo Qin,Huan-Xiang Zhou,Julie C. Mitchell,Omar N. A. Demerdash,Mayuko Takeda-Shitaka,Genki Terashi,Iain H. Moal,Xiaofan Li,Paul A. Bates,Martin Zacharias,Hahnbeom Park,Junsu Ko,Hasup Lee,Chaok Seok,Thomas Bourquard,Julie Bernauer,Anne Poupon,Jérôme Azé,Seren Soner,Şefik Kerem Ovali,Pemra Ozbek,Nir Ben Tal,Turkan Haliloglu,Howook Hwang,Thom Vreven,Brian G. Pierce,Zhiping Weng,Laura Pérez-Cano,Carles Pons,Juan Fernández-Recio,Fan Jiang,Feng Yang,Xinqi Gong,Libin Cao,Xianjin Xu,Bin Liu,Panwen Wang,Chunhua Li,Cunxin Wang,Charles H. Robert,Mainak Guharoy,Shiyong Liu,Yangyu Huang,Lin Li,Dachuan Guo,Ying Chen,Yi Xiao,Nir London,Zohar Itzhaki,Ora Schueler-Furman,Yuval Inbar,Vladimir Potapov,Mati Cohen,Gideon Schreiber,Yuko Tsuchiya,Eiji Kanamori,Daron M. Standley,Haruki Nakamura,Kengo Kinoshita,C.M. Driggers,Robert G. Hall,Jessica L. Morgan,Victor L. Hsu,Jian Zhan,Yuedong Yang,Yaoqi Zhou,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Weiyi Zhang,Carlos J. Camacho,Krishna Praneeth Kilambi,Aroop Sircar,Jeffrey J. Gray,Masahito Ohue,Nobuyuki Uchikoga,Yuri Matsuzaki,Takashi Ishida,Yutaka Akiyama,Raed Khashan,Stephen Bush,Denis Fouches,Alexander Tropsha,Juan Esquivel-Rodríguez,Daisuke Kihara,P. Benjamin Stranges,Ron Jacak,Brian Kuhlman,Sheng-You Huang,Xiaoqin Zou,Shoshana J. Wodak,Joël Janin,David Baker +97 more
TL;DR: A number of designed protein-protein interfaces with very favorable computed binding energies but which do not appear to be formed in experiments are generated, suggesting that there may be important physical chemistry missing in the energy calculations.
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The limit of accuracy of protein modeling: influence of crystal packing on protein structure.
TL;DR: A clear influence of crystal environment on protein structure, including backbone conformations, hinge-like motions and side-chain conformations is demonstrated, and a practical limit to the accuracy of protein modeling is derived.
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SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment
Vladimir Sobolev,Eran Eyal,Sergey Gerzon,Vladimir Potapov,Mariana Babor,Jaime Prilusky,Marvin Edelman +6 more
TL;DR: A suite of SPACE tools for analysis and prediction of structures of biomolecules and their complexes and includes servers and programs for structural analysis of point mutations (MutaProt), side chain modeling based on surface complementarity (SCCOMP), and construction and analysis of protein contact maps (CMA) and molecular docking software (LIGIN).