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BMC Res Notes. 2019 Jun 7;12(1):318. doi: 10.1186/s13104-019-4356-3.

Exploration of interaction scoring criteria in the CANDO platform.

Author information

1
Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St., Suite 540, Buffalo, NY, 14203, USA.
2
Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, 77 Goodell St., Suite 540, Buffalo, NY, 14203, USA. ram@compbio.org.

Abstract

OBJECTIVE:

Ascertain the optimal interaction scoring criteria for the Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun drug repurposing to improve benchmarking performance, thereby enabling more accurate prediction of novel therapeutic drug-indication pairs.

RESULTS:

We have investigated and enhanced the interaction scoring criteria in the bioinformatic docking protocol in the newest version of our platform (v1.5), with the best performing interaction scoring criterion yielding increased benchmarking accuracies from 11.7% in v1 to 12.8% in v1.5 at the top10 cutoff (the most stringent one) and correspondingly from 24.9 to 31.2% at the top100 cutoff.

KEYWORDS:

Binding site similarity; Drug repurposing; Drug-protein interaction; Molecular fingerprinting; Protein structure docking

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