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Modeling Molecular Recognition: Theory and Application

Published

Author(s)

K L. Mardis, R Luo, L David, M Potter, A J. Glemza, G F. Payne, M K. Gilson

Abstract

Efficient, reliable methods for calculating the binding affinities of noncovalent complexes would allow advances in a variety of areas such as drug discovery and separation science. We have recently described a method that accommodates significant physical detail while remaining fast enough for use in molecular design. This approach uses the predominant states method to compute free energies, an empirical force field, and an implicit solvation model based upon continuum electrostatics. We review applications of this method to a number of systems focusing on the ability of the method to accurately predict free energies of binding. The molecules discussed range from small molecules to protein-ligand complexes.
Citation
Journal of Biomolecular Structure and Dynamics
Volume
Sp.
Issue
Iss. SI

Keywords

base pair stacking, chemical separation, free energy calculations, HIV-1 protease inhibitors, molecular recognition, salt bridges

Citation

Mardis, K. , Luo, R. , David, L. , Potter, M. , Glemza, A. , Payne, G. and Gilson, M. (2008), Modeling Molecular Recognition: Theory and Application, Journal of Biomolecular Structure and Dynamics (Accessed April 20, 2024)
Created October 16, 2008