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Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
Author(s) -
Zhang Chi,
Liu Song,
Zhou Yaoqi
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20576
Subject(s) - cluster analysis , computer science , sampling (signal processing) , data mining , statistics , artificial intelligence , mathematics , filter (signal processing) , computer vision
We entered the CAPRI experiment during the middle of Round 4 and have submitted predictions for all 6 targets released since then. We used the following procedures for docking prediction: (1) the identification of possible binding region(s) of a target based on known biological information, (2) rigid‐body sampling around the binding region(s) by using the docking program ZDOCK, (3) ranking of the sampled complex conformations by employing the DFIRE‐based statistical energy function, (4) clustering based on pairwise root‐mean‐square distance and the DFIRE energy, and (5) manual inspection and relaxation of the side‐chain conformations of the top‐ranked structures by geometric constraint. Reasonable predictions were made for 4 of the 6 targets. The best fraction of native contacts within the top 10 models are 89.1% for Target 12, 54.3% for Target 13, 29.3% for Target 14, and 94.1% for Target 18. The origin of successes and failures is discussed. Proteins 2005;60:314–318. © 2005 Wiley‐Liss, Inc.