Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity

Kandel, Durga Datta and Raychaudhury, Chandan and Pal, Debnath (2014) Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity. In: JOURNAL OF MOLECULAR MODELING, 20 (4).

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Abstract

Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices) - one based solely on topological considerations without discriminating atomor bond types, and another based on topological and electronic features. We also assess their usefulness by devising a method to rank and classify molecules with regard to their antibacterial activity. Classification performances of our method are found to be superior compared to two previous studies on large heterogeneous data sets for hit finding and hit-to-lead studies even though we use much fewer parameters. It is found that for hit finding studies topological features (simple graph) alone provide significant discriminating power, and for hit-to-lead process small but consistent improvement can be made by additionally including electronic features (colored graph). Our approach is simple, interpretable, and suitable for design of molecules as we do not use any physicochemical properties. The singular use of vertex index as descriptor, novel range based feature extraction, and rigorous statistical validation are the key elements of this study.

Item Type:	Journal Article
Publication:	JOURNAL OF MOLECULAR MODELING
Publisher:	SPRINGER
Additional Information:	Copyright for this article belongs to the SPRINGER, USA
Keywords:	Chemical information; Classification; Molecular fragment descriptors; QSAR; Scoring
Department/Centre:	Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	12 Jun 2014 10:03
Last Modified:	12 Jun 2014 10:03
URI:	http://eprints.iisc.ac.in/id/eprint/49187

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