Paper Citing NAMD - Abstract
Li, Mai Suan; Binh Khanh Mai
Steered Molecular Dynamics-A Promising Tool for Drug Design
CURRENT BIOINFORMATICS, 7:342-351, DEC 2012
About 15 years ago, the steered molecular dynamics (SMD) was used to probe binding of ligand to biomolecule surfaces but in terms of drug design this approach has only recently attached attention of researchers. The main idea of using SMD to screen out leads is based on the hypothesis that the larger is the force needed to unbind a ligand from a receptor the higher its binding affinity. Thus, instead of binding free energy, the rupture force defined as the maximum on the force-time/displacement profile, is used as a score function. In this mini-review, we discuss basic concepts behind the experimental technique atomic force microscopy as well as SMD. Experimental and theoretical works on the application of SMD to the drug design problem are covered. Accumulated evidences show that SMD is as accurate as the molecular mechanics-Poisson-Boltzmann surface area method in predicting ligand binding affinity but the former is computationally much more efficient. The high correlation level between theoretically determined rupture forces and experimental data on binding energies implies that SMD is a promising tool for drug design. Our special attention is drawn to recent studies on inhibitors of influenza viruses.
