Docking and scoring with ICM: the benchmarking results and strategies for improvement.
Docking and scoring with ICM: the benchmarking results and strategies for improvement.
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DOI：
10.1007/s10822-012-9547-0
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发表时间：
2012-06
影响因子：
3.5
通讯作者：
Abagyan, Ruben
中科院分区：
文献类型：
--
作者：
Neves, Marco A. C.;Totrov, Maxim;Abagyan, Ruben
关键词：
使用内部坐标力学软件 (ICM) 进行灵活对接和评分，针对修改后的 Astex 数据集中的 85 个共晶结构进行配体结合模式预测的基准测试。 ICM 虚拟配体筛选针对 40 个 DUD 靶标基准和 11 个靶标 WOMBAT 集进行了测试。评估了每个配体结合位点的前 1 和前 3 评分姿势的自对接准确性，分别在 91% 和 95% 的预测中发现低于 2 Å RMSD 的接近天然构象。使用单刚性袋构象的虚拟配体筛选提供的 ROC 曲线下面积中值等于 69.4，其中 22.0% 的真阳性率以 2% 的假阳性率恢复。根据我们灵活的口袋细化和自付费用绑定重新评分的最佳实践，实现了高达 ROC AUC= 82.2 和 ROC(2%)= 45.2 的显着改进。通过考虑目标的多种构象可以进一步改进虚拟筛选。
Flexible docking and scoring using the Internal Coordinate Mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The ICM virtual ligand screening was tested against the 40 DUD target benchmarks and 11-target WOMBAT sets. The self-docking accuracy was evaluated for the top 1 and top 3 scoring poses at each ligand binding site with near native conformations below 2 Å RMSD found in 91% and 95% of the predictions, respectively. The virtual ligand screening using single rigid pocket conformations provided the median area under the ROC curves equal to 69.4 with 22.0% true positives recovered at 2% false positive rate. Significant improvements up to ROC AUC= 82.2 and ROC(2%)= 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target.
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影响因子：
5.7
作者：
Kufareva, Irina;Rueda, Manuel;Katritch, Vsevolod;Stevens, Raymond C.;Abagyan, Ruben;Yoshikawa, Yasushi;Furuya, Toshio;Lee, Huisun;Roy, Ambrish;Grime, John;Rebehmed, Joseph;Zhang, Yang;Roumen, Luc;de Esch, Iwan J. P.;Leurs, Rob;de Graaf, Chris;Li, Youyong;Hou, Tingjun;Mysinger, Michael M.;Weiss, Dahlia R.;Irwin, John J.;Shoichet, Brian K.;McRobb, Fiona M.;Capuano, Ben;Crosby, Ian T.;Chalmers, David K.;Yuriev, Elizabeth;Wang, Qi;Mach, Robert H.;Reichert, David E.;Chuang, Gwo-Yu;Rognan, Didier;Simms, John;Sexton, Patrick;Wootten, Denise;Latek, Dorota;Ghoshdastider, Umesh;Filipek, Slawomir;Kirkpatrick, Andrea;Trzaskowski, Bartosz;Griffith, Adam;Kim, Soo-Kyung;Abrol, Ravinder;Goddard, William A., III;Vaidehi, Nagarajan;Lam, Alfonso;Bhattacharya, Supriyo;Li, Hubert;Balaraman, Gouthaman;Niesen, Michiel;Pal, Sandeep;Vorobjev, Yrii;Bakulina, Natalia;Solovyev, Victor;Beuming, Thijs;Costanzi, Stefano;Shi, Lei;Higgs, Chris;Salam, Noeris;Lupyan, Dmitry;Sherman, Woody;Ding, Feng;Kota, Pradeep;Ramachandran, Srinivas;Dokholyan, Nikolay V.;Carlsson, Jens;Coleman, Ryan G.;Fan, Hao;Schlessinger, Avner;Sali, Andrej;Tikhonova, Irina;Pogozheva, Irina;Lomize, Andrei;Hall, Nathan E.;Muddassar, Muhammad;Zhang, Yang;Pae, Ae Nim;Lee, Jooyoung;Lopez, Laura;Obiol-Pardo, Cristian;Selent, Jana;Mahboob, Sadia;Werner, Tim;Church, W. Bret;Brylinski, Michal;Ando, Tadashi;Guerler, Aysam;Zhou, Hongyi;Skolnick, Jeffrey;Xhaard, Henri;Jurkowski, Wiktor;Elofsson, Arne;Murad, Ahsan K.;Drwal, Malgorzata;Dupree, Tom B.;Griffith, Renate;Ostopovici-Halip, Liliana;Bologa, Cristian;Chen, K. M.;Sun, J.;Barth, Patrick;Yarov-Yarovoy, Vladimir;Baker, David;Vroling, Bas;Sanders, Marijn P. A.;Nabuurs, Sander B.;Nikiforovich, Gregory V.
通讯作者：
Nikiforovich, Gregory V.
影响因子：
2.9
作者：
Irwin, JJ;Raushel, FM;Shoichet, BK
通讯作者：
Shoichet, BK
影响因子：
7.3
作者：
Moitessier, N.;Englebienne, P.;Corbeil, C. R.
通讯作者：
Corbeil, C. R.
影响因子：
2.7
作者：
Doennecke, Daniel;Schweinitz, Andrea;Steinmetzer, Torsten
通讯作者：
Steinmetzer, Torsten
影响因子：
7.3
作者：
Katritch V;Jaakola VP;Lane JR;Lin J;Ijzerman AP;Yeager M;Kufareva I;Stevens RC;Abagyan R
通讯作者：
Abagyan R