J
João P. G. L. M. Rodrigues
Researcher at Stanford University
Publications - 63
Citations - 4912
João P. G. L. M. Rodrigues is an academic researcher from Stanford University. The author has contributed to research in topics: Macromolecular docking & Protein Data Bank. The author has an hindex of 22, co-authored 60 publications receiving 3370 citations. Previous affiliations of João P. G. L. M. Rodrigues include University of Aveiro & Utrecht University.
Papers
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Journal ArticleDOI
The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
G. C. P. van Zundert,João P. G. L. M. Rodrigues,Mikael Trellet,Christophe Schmitz,Panagiotis L. Kastritis,Ezgi Karaca,Adrien S. J. Melquiond,M. van Dijk,S.J. de Vries,Alexandre M. J. J. Bonvin +9 more
TL;DR: The updated version 2.2.2 of the HADDOCK portal is presented, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface.
Journal ArticleDOI
PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
Li C. Xue,João P. G. L. M. Rodrigues,Panagiotis L. Kastritis,Alexandre M. J. J. Bonvin,Anna Vangone +4 more
TL;DR: Protein binDIng enerGY prediction (PRODIGY), a web server to predict the binding affinity of protein-protein complexes from their 3D structure based on intermolecular contacts and properties derived from non-interface surface is presented.
Journal ArticleDOI
Sequence co-evolution gives 3D contacts and structures of protein complexes
Thomas A. Hopf,Charlotta P I Schärfe,Charlotta P I Schärfe,João P. G. L. M. Rodrigues,Anna G. Green,Oliver Kohlbacher,Chris Sander,Alexandre M. J. J. Bonvin,Debora S. Marks +8 more
TL;DR: Analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes, and predicts protein–protein contacts in 32 complexes of unknown structure.
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
Structural insights into binding specificity, efficacy and bias of a beta2AR partial agonist.
Matthieu Masureel,Yaozhong Zou,Louis Picard,Emma T van der Westhuizen,Emma T van der Westhuizen,Jacob P. Mahoney,João P. G. L. M. Rodrigues,Thomas J. Mildorf,Ron O. Dror,David E. Shaw,Michel Bouvier,Els Pardon,Jan Steyaert,Roger K. Sunahara,William I. Weis,Cheng Zhang,Brian K. Kobilka +16 more
TL;DR: The active-state structure of a GPCR occupied by a partial agonist, β2AR with salmeterol, together with mutagenesis and biophysical studies, explains this ligand's unusual pharmacological profile.