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Evaluation of the 3D‐Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial
Author(s) -
Smith Graham R.,
Sternberg Michael J.E.
Publication year - 2003
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.10396
Subject(s) - dock , suite , superimposition , computer science , docking (animal) , artificial intelligence , medicine , biology , geography , biochemistry , archaeology , nursing
The 3D‐Dock suite of programs has been used to make predictions for the seven targets in rounds 1 and 2 of the CAPRI method evaluation exercise. Some correct contacts were obtained in at least one prediction for four of seven targets. Target 06 was predicted very well, with an RMSD of the ligand after superimposition of the receptor of only 0.77 Å. We investigate the performance of the various stages of the method, with the aim of finding where improvements need to be made, and in particular whether the manual interventions that were made were essential, and whether results of the level of accuracy obtained for target 06 may be expected with confidence. Proteins 2003;52:74–79. © 2003 Wiley‐Liss, Inc.