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Omagari K, Mitomo D, Kubota S, et al. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Adv Appl Bioinform Chem. 2008;1:19-28doi: 10.2147/aabc.s3767.
Omagari, K., Mitomo, D., Kubota, S., Nakamura, H., & Fukunishi, Y. (2008). A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Advances and applications in bioinformatics and chemistry : AABC, 119-28. https://doi.org/10.2147/aabc.s3767
Omagari, Katsumi, et al. "A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening." Advances and applications in bioinformatics and chemistry : AABC vol. 1 (2008): 19-28. doi: https://doi.org/10.2147/aabc.s3767
Omagari K, Mitomo D, Kubota S, Nakamura H, Fukunishi Y. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Adv Appl Bioinform Chem. 2008;1:19-28. doi: 10.2147/aabc.s3767. Epub 2008 Aug 12. PMID: 21918604; PMCID: PMC3169939.
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Adv Appl Bioinform Chem. 2008;1:19-28. doi: 10.2147/aabc.s3767. Epub 2008 Aug 12.

A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

Advances and applications in bioinformatics and chemistry : AABC

Katsumi Omagari, Daisuke Mitomo, Satoru Kubota, Haruki Nakamura, Yoshifumi Fukunishi

Affiliations

  1. Japan Biological Informatics Consortium (JBiC), Koto-ku, Tokyo, Japan.

PMID: 21918604 PMCID: PMC3169939 DOI: 10.2147/aabc.s3767

Abstract

We examined the procedures to combine two different in silico drug-screening results to achieve a high hit ratio. When the 3D structure of the target protein and some active compounds are known, both structure-based and ligand-based in silico screening methods can be applied. In the present study, the machine-learning score modification multiple target screening (MSM-MTS) method was adopted as a structure-based screening method, and the machine-learning docking score index (ML-DSI) method was adopted as a ligand-based screening method. To combine the predicted compound's sets by these two screening methods, we examined the product of the sets (consensus set) and the sum of the sets. As a result, the consensus set achieved a higher hit ratio than the sum of the sets and than either individual predicted set. In addition, the current combination was shown to be robust enough for the structural diversities both in different crystal structure and in snapshot structures during molecular dynamics simulations.

Keywords: conformation of active site; consensus score; in silico; protein-based screening; protein-ligand docking; screening

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