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J Comput Aided Mol Des. 2006 Apr;20(4):237-48. Epub 2006 Jun 21.

A virtual active compound produced from the negative image of a ligand-binding pocket, and its application to in-silico drug screening.

Author information

1
Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. y-fukunishi@jbirc.aist.go.jp

Abstract

We developed a new structure-based in-silico screening method using a negative image of a ligand-binding pocket and a multi-protein-compound interaction matrix. Based on the structure of the ligand pocket of the target protein, we designed a negative image, which consists of virtual atoms whose radii are close to those of carbon atoms. The virtual atoms fit the pocket ideally and achieve an optimal Coulomb interaction. A protein-compound docking program calculates the protein-compound interaction matrix for many proteins and many compounds including the negative image, which can be treated as a virtual compound. With specific attention to a vector of docking scores for a single compound with many proteins, we selected a compound whose score vector was similar to that of the negative image as a candidate hit compound. This method was applied to representative target proteins and showed high database enrichment with a relatively quick procedure.

PMID:
16897580
DOI:
10.1007/s10822-006-9047-1
[Indexed for MEDLINE]

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