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J Chem Inf Model. 2006 Sep-Oct;46(5):2071-84.

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening.

Author information

1
Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan. y-fukunishi@jbirc.aist.go.jp

Abstract

We developed a new method to improve the accuracy of molecular interaction data using a molecular interaction matrix. This method was applied to enhance the database enrichment of in silico drug screening and in silico target protein screening using a protein-compound affinity matrix calculated by a protein-compound docking software. Our assumption was that the protein-compound binding free energy of a compound could be improved by a linear combination of its docking scores with many different proteins. We proposed two approaches to determine the coefficients of the linear combination. The first approach is based on similarity among the proteins, and the second is a machine-learning approach based on the known active compounds. These methods were applied to in silico screening of the active compounds of several target proteins and in silico target protein screening.

PMID:
16995738
DOI:
10.1021/ci060152z
[Indexed for MEDLINE]

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