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Reddy, M. R. and Reddy, C. R. (2014) Free Energy Calculations to Estimate Ligand-Binding Affinities in Structure-Based Drug Design. Current Pharmaceutical Design, 20 (20). pp. 3323-3337.

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Post-genomic era has led to the discovery of several new targets posing challenges for structure-based drug design efforts to identify lead compounds. Multiple computational methodologies exist to predict the high ranking hit/lead compounds. Among them, free energy methods provide the most accurate estimate of predicted binding affinity. Pathway-based Free Energy Perturbation (FEP), Thermodynamic Integration (TI) and Slow Growth (SG) as well as less rigorous end-point methods such as Linear interaction energy (LIE), Molecular Mechanics-Poisson Boltzmann./Generalized Born Surface Area (MM-PBSA/GBSA) and lambda-dynamics have been applied to a variety of biologically relevant problems. The recent advances in free energy methods and their applications including the prediction of protein-ligand binding affinity for some of the important drug targets have been elaborated. Results using a recently developed Quantum Mechanics (QM)/Molecular Mechanics (MM) based Free Energy Perturbation (FEP) method, which has the potential to provide a very accurate estimation of binding affinities to date has been discussed. A case study for the optimization of inhibitors for the fructose 1,6-bisphosphatase inhibitors has been described.

Item Type: Article
Subjects: Animal Genetics and Genomics
Depositing User: Unnamed user with email alok@urdip.res.in
Date Deposited: 18 Mar 2015 06:18
Last Modified: 18 Mar 2015 06:23
URI: http://niab.sciencecentral.in/id/eprint/6

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