Development and testing of an automated approach to protein docking

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Abstract
A new version of GRAMM was applied to Targets 14, 18, and 19 in CAPRI Round 5. The predictions were generated without manual intervention. Ten top-ranked matches for each target were submitted. The docking was performed by a rigid-body procedure with a smoothed potential function to accommodate conformational changes. The first stage was a global search on a fine grid with a projection of a smoothed Lennard–Jones potential. The top predictions from the first stage were subjected to the conjugate gradient minimization with the same smoothed potential. The resulting local minima were reranked according to the weighted sum of Lennard–Jones potential, pairwise residue–residue statistical preferences, cluster occupancy, and the degree of the evolutionary conservation of the predicted interface. For Targets 14 and 18, the conformation of the complex was predicted with root-mean-square deviation (RMSD) of the ligand interface atoms 0.68 Å and 1.88 Å correspondingly. For Target 19, the interface areas on both proteins were correctly predicted. The performance of the procedure was also analyzed on the benchmark of bound–unbound protein complexes. The results show that, on average, conformations of only 3 side-chains need to be optimized during docking of unbound structures before the backbone changes become a limiting factor. The GRAMM-X docking server is available for public use at http://www.bioinformatics.ku.edu. Proteins 2005;60:296–301.