Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Modeling Molecular Recognition: Theory and Application



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


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.
Journal of Biomolecular Structure and Dynamics
Iss. SI


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


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