NDLI: KNNsim: k-Nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules

Content Provider	Springer Nature Link
Author	Plewczynski, Dariusz
Copyright Year	2008
Abstract	Protein targets specificity classification is an important step in computational drug development and design efforts. The enhanced classification models of small chemical molecules enable the rapid scanning of large compounds databases. Here, we present the k-nearest neighbors with genetic algorithm feature optimization approach for selection of small molecule protein inhibitors. The method is trained on selected, diverse activity classes of the MDL drug data report (MDDR) with ligands described using simple atom pairs two dimensional chemical descriptors. The accuracy of inhibitors identification is presented in confusion tables with calculated recall and precision values. The precision for selected types of targets exceeded 70%, and the recall reaches 40%. As a consequence, the method can be easily applied to large commercial compounds collections in a drug development campaign in order to significantly reduce the number of ligands for further costly experimental validation.
Starting Page	591
Ending Page	596
Page Count	6
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	15
Issue Number	6
e-ISSN	09485023
Language	English
Publisher	Springer-Verlag
Publisher Date	2008-07-29
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Chemical descriptors Compound identification Machine-learning methods MDL drug data report Protein target specificity Substrate specificity Virtual high-throughput screening Computer Application in Life Sciences Life Sciences Health Informatics Molecular Medicine Biomedicine general Computer Applications in Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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