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J Chem Inf Model. 2011 Jun 27;51(6):1423-30. doi: 10.1021/ci200098v. Epub 2011 May 11.

MiniMuDS: a new optimizer using knowledge-based potentials improves scoring of docking solutions.

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Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marburg, Germany.


In small molecule docking, the scoring and ranking of generated conformations is an important, though still not a completely resolved problem. Rescoring schemes often improve the quality of the obtained rankings. It is known that a local optimization is essential before a valid rescore value can be calculated. Here, we present a method that improves rescoring results obtained with the DrugScore function due to a new optimization technique. The method implements a more sophisticated search algorithm compared to the classic local optimization procedures used in this context. We validated the proposed method on a set of 192 protein-ligand complexes. Results show substantial improvements compared to original docking results with success rates increased by up to 10% for top scored solutions below 2 Å root-mean-square deviation to the native state and up to 18% increase below 1 Å, respectively.

[Indexed for MEDLINE]

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