Title :

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Author(s) :

Lensink, Marc [Auteur]
Velankar, Sameer [Auteur]
Kryshtafovych, Andriy [Auteur]
Huang, Shen-You [Auteur]
Schneidman-Duhovny, Dina [Auteur]
Sali, Andrej [Auteur]
Segura, Joan [Auteur]
Fernandez-Fuentes, Narcis [Auteur]
Viswanath, Shruthi [Auteur]
Elber, Ron [Auteur]
Grudinin, Sergei [Auteur]
Popov, Petr [Auteur]
Neveu, Emilie [Auteur]
Lee, Hasup [Auteur]
Baek, Minkyung [Auteur]
Park, Sangwoo [Auteur]
Heo, Lim [Auteur]
Rie Lee, Gyu [Auteur]
Seok, Chaok [Auteur]
Qin, Sanbo [Auteur]
Zhou, Huan-Xiang [Auteur]
Ritchie, David W. [Auteur]
Maigret, Bernard [Auteur]
Devignes, Marie-Dominique [Auteur]
Ghoorah, Anisah [Auteur]
Torchala, Mieczyslaw [Auteur]
Chaleil, Raphaël A. G. [Auteur]
Bates, Paul A. [Auteur]
Ben-Zeev, Efrat [Auteur]
Eisenstein, Miriam [Auteur]
Negi, Surendra S. [Auteur]
Weng, Zhiping [Auteur]
Vreven, Thom [Auteur]
Pierce, Brian G. [Auteur]
Borrman, Tyler M. [Auteur]
Yu, Jinchao [Auteur]
Ochsenbein, Françoise [Auteur]
Guerois, Raphaël [Auteur]
Vangone, Anna [Auteur]
Rodrigues, João P. G. L. M. [Auteur]
van Zundert, Gydo [Auteur]
Nellen, Mehdi [Auteur]
Xue, Li [Auteur]
Karaca, Ezgi [Auteur]
Melquiond, Adrien S. J. [Auteur]
Visscher, Koen [Auteur]
Kastritis, Panagiotis L. [Auteur]
Bonvin, Alexandre M. J. J. [Auteur]
Xu, Xianjin [Auteur]
Qiu, Liming [Auteur]
Yan, Chengfei [Auteur]
Li, Jilong [Auteur]
Ma, Zhiwei [Auteur]
Cheng, Jianlin [Auteur]
Zou, Xiaoqin [Auteur]
Shen, Yang [Auteur]
Peterson, Lenna X. [Auteur]
Kim, Hyung-Rae [Auteur]
Roy, Amit [Auteur]
Han, Xusi [Auteur]
Esquivel-Rodriguez, Juan [Auteur]
Kihara, Daisuke [Auteur]
Yu, Xiaofeng [Auteur]
Bruce, Neil J. [Auteur]
Fuller, Jonathan C. [Auteur]
Wade, Rebecca C. [Auteur]
Anishchenko, Ivan [Auteur]
Kundrotas, Petras J. [Auteur]
Vakser, Ilya A. [Auteur]
Imai, Kenichiro [Auteur]
Yamada, Kazunori [Auteur]
Oda, Toshiyuki [Auteur]
Nakamura, Tsukasa [Auteur]
Tomii, Kentaro [Auteur]
Pallara, Chiara [Auteur]
Romero-Durana, Miguel [Auteur]
Jiménez-García, Brian [Auteur]
Moal, Iain H. [Auteur]
Fernández-Recio, Juan [Auteur]
Joung, Jong Young [Auteur]
Kim, Jong Yun [Auteur]
Joo, Keehyoung [Auteur]
Lee, Jooyoung [Auteur]
Kozakov, Dima [Auteur]
Vajda, Sandor [Auteur]
Mottarella, Scott [Auteur]
Hall, David R. [Auteur]
Beglov, Dmitri [Auteur]
Mamonov, Artem [Auteur]
Xia, Bing [Auteur]
Bohnuud, Tanggis [Auteur]
Del Carpio, Carlos A. [Auteur]
Ichiishi, Eichiro [Auteur]
Marze, Nicholas [Auteur]
Kuroda, Daisuke [Auteur]
Roy Burman, Shourya S. [Auteur]
Gray, Jeffrey J. [Auteur]
Chermak, Edrisse [Auteur]
Cavallo, Luigi [Auteur]
Oliva, Romina [Auteur]
Tovchigrechko, Andrey [Auteur]
Wodak, Shoshana J. [Auteur]

Journal title :

Proteins

Abbreviated title :

Proteins

Volume number :

84

Pages :

323-348

Publication date :

2016-09

ISSN :

1097-0134

English keyword(s) :

protein docking
Humans
Protein Multimerization
Proteins
Thermodynamics
Bacteria
Protein Interaction Domains and Motifs
Binding Sites
Protein Structure, Tertiary
Protein Conformation, alpha-Helical
CASP
Computational Biology
oligomer state
International Cooperation
Models, Statistical
Protein interactions
Molecular Dynamics Simulation
Protein Folding
Amino Acid Motifs
Sequence Homology, Amino Acid
Algorithms
Capri
Protein Conformation, beta-Strand
Protein Binding
Blind prediction
Molecular Docking Simulation
Software
Internet

HAL domain(s) :

Chimie/Chimie théorique et/ou physique

English abstract : [en]

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets ...
Show more >We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. 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. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy. Proteins 2016; 84(Suppl 1):323-348. © 2016 Wiley Periodicals, Inc.Show less >

Language :

Anglais

Administrative institution(s) :

CNRS
Université de Lille

Collections :

• Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) - UMR 8576

Research team(s) :

Computational Molecular Systems Biology

Submission date :

2020-02-12T16:20:22Z