A swift all-atom energy-based computational protocol to predict DNA-ligand binding affinity and DeltaTm.

Abstract

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 (R2 = 0.90) and 0.96 (R2 = 0.93) in linear plots against experimental binding free energies (DeltaGo) and DeltaTm, respectively. The protocol is translated into a swift, web-enabled, freely accessible computational tool, http://www.scfbio-iitd.res.in/preddicta, for DeltaGo and DeltaTm prediction for DNA-ligand complexes to aid and expedite rational drug design attempts.

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@article{Shaikh2007ASA, title={A swift all-atom energy-based computational protocol to predict DNA-ligand binding affinity and DeltaTm.}, author={Saher Afshan Shaikh and Bhyravabhotla Jayaram}, journal={Journal of medicinal chemistry}, year={2007}, volume={50 9}, pages={2240-4} }