Path-integral method for predicting relative binding affinities of protein-ligand complexes.

ABSTRACT: We present a novel approach for computing biomolecular interaction binding affinities based on a simple path integral solution of the Fokker-Planck equation. Computing the free energy of protein-ligand interactions can expedite structure-based drug design. Traditionally, the problem is seen through the lens of statistical thermodynamics. The computations can become, however, prohibitively long for the change in the free energy upon binding to be determined accurately. In this work, we present a different approach based on a stochastic kinetic formalism. Inspired by Feynman's path integral formulation, we extend the theory to classical interacting systems. The ligand is modeled as a Brownian particle subjected to the effective nonbonding interaction potential of the receptor. This allows th

SUBMITTER: Mulakala C 

PROVIDER: S-EPMC2671935 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature