Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
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DOI：
10.1002/prot.25007
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发表时间：
2016-09
影响因子：
2.9
通讯作者：
Wodak, Shoshana J.
中科院分区：
文献类型：
--
作者：
Lensink, Marc F.;Velankar, Sameer;Kryshtafovych, Andriy;Huang, Shen-You;Schneidman-Duhovny, Dina;Sali, Andrej;Segura, Joan;Fernandez-Fuentes, Narcis;Viswanath, Shruthi;Elber, Ron;Grudinin, Sergei;Popov, Petr;Neveu, Emilie;Lee, Hasup;Baek, Minkyung;Park, Sangwoo;Heo, Lim;Lee, Gyu Rie;Seok, Chaok;Qin, Sanbo;Zhou, Huan-Xiang;Ritchie, David W.;Maigret, Bernard;Devignes, Marie-Dominique;Ghoorah, Anisah;Torchala, Mieczyslaw;Chaleil, Raphael A. G.;Bates, Paul A.;Ben-Zeev, Efrat;Eisenstein, Miriam;Negi, Surendra S.;Weng, Zhiping;Vreven, Thom;Pierce, Brian G.;Borrman, Tyler M.;Yu, Jinchao;Ochsenbein, Francoise;Guerois, Raphael;Vangone, Anna;Rodrigues, Joao P. G. L. M.;van Zundert, Gydo;Nellen, Mehdi;Xue, Li;Karaca, Ezgi;Melquiond, Adrien S. J.;Visscher, Koen;Kastritis, Panagiotis L.;Bonvin, Alexandre M. J. J.;Xu, Xianjin;Qiu, Liming;Yan, Chengfei;Li, Jilong;Ma, Zhiwei;Cheng, Jianlin;Zou, Xiaoqin;Shen, Yang;Peterson, Lenna X.;Kim, Hyung-Rae;Roy, Amit;Han, Xusi;Esquivel-Rodriguez, Juan;Kihara, Daisuke;Yu, Xiaofeng;Bruce, Neil J.;Fuller, Jonathan C.;Wade, Rebecca C.;Anishchenko, Ivan;Kundrotas, Petras J.;Vakser, Ilya A.;Imai, Kenichiro;Yamada, Kazunori;Oda, Toshiyuki;Nakamura, Tsukasa;Tomii, Kentaro;Pallara, Chiara;Romero-Durana, Miguel;Jimenez-Garcia, Brian;Moal, Iain H.;Fernandez-Recio, Juan;Joung, Jong Young;Kim, Jong Yun;Joo, Keehyoung;Lee, Jooyoung;Kozakov, Dima;Vajda, Sandor;Mottarella, Scott;Hall, David R.;Beglov, Dmitri;Mamonov, Artem;Xia, Bing;Bohnuud, Tanggis;Del Carpio, Carlos A.;Ichiishi, Eichiro;Marze, Nicholas;Kuroda, Daisuke;Burman, Shourya S. Roy;Gray, Jeffrey J.;Chermak, Edrisse;Cavallo, Luigi;Oliva, Romina;Tovchigrechko, Andrey;Wodak, Shoshana J.
我们介绍了第一个CAPRI第30轮的结果，这是第一个联合CASP -CAPRI实验，该实验从蛋白质结构预测和蛋白质 - 蛋白质对接群落中汇集了专家。靶标主要包括同型二聚体，一些同二二聚体和两个异二聚体，以及包含蛋白质链，可以很容易地使用模板进行建模从蛋白质数据库中，对每个目标的24个CAPRI组和7个CASP组提交了对接的预测，并且每个目标的CAPRI组参与了CAPRI评分实验。目标络合物的结果表明，通过同源模型和对接计算的同型二聚体组件的预测非常成功对于这些人来说，实现了更差的预测性能，而通常提供有用的支持，以模棱两可或不准确的寡聚状态分配，通常以晶体接触式界面为特征。对于真正的四聚体目标，预测性能非常差，其中不准确同源性的亚基模型和较小的成对式接口严重限制了我们的分析能力。始终以可接受的蛋白质确定其关联模式。 Wiley Werdionals，Inc。发表的结构，功能和生物信息学
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 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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影响因子：
2.9
作者：
Lensink MF;Moal IH;Bates PA;Kastritis PL;Melquiond AS;Karaca E;Schmitz C;van Dijk M;Bonvin AM;Eisenstein M;Jiménez-García B;Grosdidier S;Solernou A;Pérez-Cano L;Pallara C;Fernández-Recio J;Xu J;Muthu P;Praneeth Kilambi K;Gray JJ;Grudinin S;Derevyanko G;Mitchell JC;Wieting J;Kanamori E;Tsuchiya Y;Murakami Y;Sarmiento J;Standley DM;Shirota M;Kinoshita K;Nakamura H;Chavent M;Ritchie DW;Park H;Ko J;Lee H;Seok C;Shen Y;Kozakov D;Vajda S;Kundrotas PJ;Vakser IA;Pierce BG;Hwang H;Vreven T;Weng Z;Buch I;Farkash E;Wolfson HJ;Zacharias M;Qin S;Zhou HX;Huang SY;Zou X;Wojdyla JA;Kleanthous C;Wodak SJ
通讯作者：
Wodak SJ
影响因子：
7.7
作者：
Ovchinnikov S;Kamisetty H;Baker D
通讯作者：
Baker D
影响因子：
2.9
作者：
Kryshtafovych, Andriy;Monastyrskyy, Bohdan;Fidelis, Krzysztof
通讯作者：
Fidelis, Krzysztof
影响因子：
5.6
作者：
Dey, Sucharita;Pal, Arumay;Janin, Joel
通讯作者：
Janin, Joel
DOI：
10.1073/pnas.1200678109
发表时间：
2012-06-12
影响因子：
11.1
作者：
Kundrotas, Petras J.;Zhu, Zhengwei;Vakser, Ilya A.
通讯作者：
Vakser, Ilya A.