Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial

Proteins
Graham R SmithCAPRI blind trial

Abstract

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 A. 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.

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Citations

Apr 20, 2004·Current Opinion in Structural Biology·Shoshana J Wodak, Raúl Méndez
Feb 17, 2005·Bioinformatics·Carlos J Camacho, Chao Zhang
Jun 11, 2004·BMC Bioinformatics·Drew LettFrederic Pio
Oct 30, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ganesh S AnandElizabeth A Komives
Jun 15, 2007·Journal of Molecular Graphics & Modelling·Vasu ChandrasekaranEthan Will Taylor
Jun 28, 2005·Proteins·Phil CarterMichael J E Sternberg
Oct 7, 2005·Proteins·Philipp HeuserDietmar Schomburg
May 23, 2009·Journal of Computational Chemistry·Irina S MoreiraMaria J Ramos
Apr 1, 2013·Intrinsically Disordered Proteins·Vishnu Priyanka Reddy ChichiliJ Sivaraman

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