J
Juan Esquivel-Rodríguez
Researcher at Purdue University
Publications - 23
Citations - 932
Juan Esquivel-Rodríguez is an academic researcher from Purdue University. The author has contributed to research in topics: Macromolecular docking & Protein structure prediction. The author has an hindex of 14, co-authored 22 publications receiving 789 citations. Previous affiliations of Juan Esquivel-Rodríguez include Costa Rica Institute of Technology.
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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.
Journal ArticleDOI
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Marc F. Lensink,Sameer Velankar,Andriy Kryshtafovych,Shen You Huang,Dina Schneidman-Duhovny,Andrej Sali,Joan Segura,Narcis Fernandez-Fuentes,Shruthi Viswanath,Ron Elber,Sergei Grudinin,Petr Popov,Emilie Neveu,Hasup Lee,Minkyung Baek,Sangwoo Park,Lim Heo,Gyu Rie Lee,Chaok Seok,Sanbo Qin,Huan-Xiang Zhou,David W. Ritchie,Bernard Maigret,Marie-Dominique Devignes,Anisah W. Ghoorah,Mieczyslaw Torchala,Raphael A. G. Chaleil,Paul A. Bates,Efrat Ben-Zeev,Miriam Eisenstein,Surendra S. Negi,Zhiping Weng,Thom Vreven,Brian G. Pierce,Tyler M. Borrman,Jinchao Yu,Françoise Ochsenbein,Raphael Guerois,Anna Vangone,João P. G. L. M. Rodrigues,Gydo C. P. van Zundert,Mehdi Nellen,Li C. Xue,Ezgi Karaca,Adrien S. J. Melquiond,Koen M. Visscher,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Xianjin Xu,Liming Qiu,Chengfei Yan,Jilong Li,Zhiwei Ma,Jianlin Cheng,Xiaoqin Zou,Yang Shen,Lenna X. Peterson,Hyung Rae Kim,Amit Roy,Amit Roy,Xusi Han,Juan Esquivel-Rodríguez,Daisuke Kihara,Xiaofeng Yu,Neil J. Bruce,Jonathan C. Fuller,Rebecca C. Wade,Ivan Anishchenko,Petras J. Kundrotas,Ilya A. Vakser,Kenichiro Imai,Kazunori D. Yamada,Toshiyuki Oda,Tsukasa Nakamura,Kentaro Tomii,Chiara Pallara,Miguel Romero-Durana,Brian Jiménez-García,Iain H. Moal,Juan Fernández-Recio,Jong Young Joung,Jong Yun Kim,Keehyoung Joo,Jooyoung Lee,Jooyoung Lee,Dima Kozakov,Sandor Vajda,Scott E. Mottarella,David R. Hall,Dmitri Beglov,Artem B. Mamonov,Bing Xia,Tanggis Bohnuud,Carlos A. Del Carpio,Carlos A. Del Carpio,Eichiro Ichiishi,Nicholas A. Marze,Daisuke Kuroda,Shourya S. Roy Burman,Jeffrey J. Gray,Edrisse Chermak,Luigi Cavallo,Romina Oliva,Andrey Tovchigrechko,Shoshana J. Wodak +104 more
TL;DR: Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations, and that docking procedures tend to perform better than standard homology modeled techniques.
Journal ArticleDOI
Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions
Rocco Moretti,Sarel J. Fleishman,Rudi Agius,Mieczyslaw Torchala,Paul A. Bates,Panagiotis L. Kastritis,João P. G. L. M. Rodrigues,Mikael Trellet,Alexandre M. J. J. Bonvin,Meng Cui,Marianne Rooman,Dimitri Gillis,Yves Dehouck,Iain H. Moal,Miguel Romero-Durana,Laura Pérez-Cano,Chiara Pallara,Brian Jimenez,Juan Fernández-Recio,Samuel C. Flores,Michael S. Pacella,Krishna Praneeth Kilambi,Jeffrey J. Gray,Petr Popov,Petr Popov,Sergei Grudinin,Sergei Grudinin,Juan Esquivel-Rodríguez,Daisuke Kihara,Nan Zhao,Dmitry Korkin,Xiaolei Zhu,Omar N. A. Demerdash,Julie C. Mitchell,Eiji Kanamori,Yuko Tsuchiya,Haruki Nakamura,Hasup Lee,Hahnbeom Park,Chaok Seok,Jamica Sarmiento,Shide Liang,Shusuke Teraguchi,Daron M. Standley,Hiromitsu Shimoyama,Genki Terashi,Mayuko Takeda-Shitaka,Mitsuo Iwadate,Hideaki Umeyama,Dmitri Beglov,David R. Hall,Dima Kozakov,Sandor Vajda,Brian G. Pierce,Howook Hwang,Thom Vreven,Zhiping Weng,Yangyu Huang,Haotian Li,Xiufeng Yang,Xiaofeng Ji,Shiyong Liu,Yi Xiao,Martin Zacharias,Sanbo Qin,Huan-Xiang Zhou,Sheng-You Huang,Xiaoqin Zou,Sameer Velankar,Joël Janin,Shoshana J. Wodak,David Baker +71 more
TL;DR: A community‐wide assessment of methods to predict the effects of mutations on protein–protein interactions found that large‐scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.
Journal ArticleDOI
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.
TL;DR: The 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces, is introduced, a series expansion of mathematical three-dimensional function which allows rapid comparison of surface shapes, which is sufficient for real-time structure database screening.
Journal ArticleDOI
Multi-LZerD: multiple protein docking for asymmetric complexes.
TL;DR: A novel computational multiple protein docking algorithm, Multi‐LZerD, that builds models of multimeric complexes by effectively reusing pairwise docking predictions of component proteins, and was able to predict near‐native structures for multimerics complexes of various topologies.