ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.
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DOI：
10.1002/prot.25887
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发表时间：
2020-08
期刊：
影响因子：
2.9
通讯作者：
Kozakov D
中科院分区：
文献类型：
--
作者：
Padhorny D;Porter KA;Ignatov M;Alekseenko A;Beglov D;Kotelnikov S;Ashizawa R;Desta I;Alam N;Sun Z;Brini E;Dill K;Schueler-Furman O;Vajda S;Kozakov D
蛋白质对接实验中的目标CAPRI通常提出新的挑战，并为方法论的新发展做出了贡献。在CAPRI的第38-45轮中（对预测相互作用的批判性评估）基于模板的方法（TBM）已成功地模拟了可用的模板。但是，对于弱或模棱两可的模板，需要集成自由对接和基于模板的方法。我们证明，使用cluspro的自由对接可以重现弱或模棱两可的模板所建议的，同时又不重现其他界面，从而可以帮助选择模板，从而产生最佳模型。在其他情况下，免费对接可能会揭示是否有任何可用模板可能提供近乎本地的界面。我们讨论将基于模板的建模与传统免费对接结合的潜在优势。还提出了结果，以证明Cluspro TBM服务器纯粹基于模板的建模可以为具有至少一个生产模板的目标产生相当准确的模型。新服务器可在https://tbm.cluspro.org上免费使用。
Targets in the protein docking experiment CAPRI generally present new challenges and contribute to new developments in methodology. In rounds 38-45 of CAPRI (Critical Assessment of PRedicted Interactions) template-based methods (TBMs) have been used with success for modeling complexes for which good templates were available. For weak or ambiguous templates however, integrating free docking and template-based methods becomes necessary. We demonstrate that free docking using ClusPro can reproduce some interfaces suggested by weak or ambiguous templates while not reproducing others, and thereby can help to choose the template resulting in the best model. In other cases free docking may reveal if none of the available templates is likely to provide a near-native interface. We discuss the potential advantages of combining template-based modeling with traditional free docking. Results are also presented to demonstrate that purely template-based modeling by the ClusPro TBM server can yield fairly accurate models for targets with at least one productive template. The new server is freely available for non-commercial use at https://tbm.cluspro.org.
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影响因子：
2.9
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.
通讯作者：
Wodak, Shoshana J.
影响因子：
14.8
作者：
Kozakov D;Hall DR;Xia B;Porter KA;Padhorny D;Yueh C;Beglov D;Vajda S
通讯作者：
Vajda S
影响因子：
14.9
作者：
Comeau, SR;Gatchell, DW;Camacho, CJ
通讯作者：
Camacho, CJ
影响因子：
2.9
作者：
Lensink, Marc F.;Nadzirin, Nurul;Wodak, Shoshana J.
通讯作者：
Wodak, Shoshana J.
DOI：
10.1007/978-1-59745-398-1_30
发表时间：
2008-01-01
期刊：
FUNCTIONAL PROTEOMICS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Keskin, Ozlem;Nussinov, Ruth;Gursoy, Attila
通讯作者：
Gursoy, Attila