A Swift All-Atom Energy-Based Computational Protocol to Predict DNA−Ligand Binding Affinity and ΔT m

A hybrid molecular mechanics−statistical mechanics−solvent accessibility-based computational protocol is developed to calculate DNA−ligand binding affinity without any database training and is validated on 50 DNA−ligand complexes. The calculated binding energies yield high correlation coefficients o...

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Bibliographic Details
Published in:Journal of medicinal chemistry 2007-05, Vol.50 (9), p.2240-2244
Main Authors: Shaikh, Saher Afshan, Jayaram, B
Format: Article
Language:English
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Summary:A hybrid molecular mechanics−statistical mechanics−solvent accessibility-based computational protocol is developed to calculate DNA−ligand binding affinity without any database training and is validated on 50 DNA−ligand complexes. The calculated binding energies yield high correlation coefficients of 0.95 (R 2 = 0.90) and 0.96 (R 2 = 0.93) in linear plots against experimental binding free energies (ΔG o) and ΔT m, respectively. The protocol is translated into a swift, web-enabled, freely accessible computational tool, http://www.scfbio-iitd.res.in/preddicta, for ΔG o and ΔT m prediction for DNA−ligand complexes to aid and expedite rational drug design attempts.
ISSN:0022-2623
1520-4804
DOI:10.1021/jm060542c