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- Title
A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening.
- Authors
Fukunishi, Yoshifumi; Kubota, Satoru; Kanai, Chisato; Nakamura, Haruki
- 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.
- Subjects
LIGANDS (Biochemistry); PROTEINS; DRUGS; CONFORMATIONAL analysis; VIRTUAL machine systems; COMPUTER input-output equipment
- Publication
Journal of Computer-Aided Molecular Design, 2006, Vol 20, Issue 4, p237
- ISSN
0920-654X
- Publication type
Article
- DOI
10.1007/s10822-006-9047-1