Significant enhancement of docking sensitivity using implicit ligand sampling.

ABSTRACT: The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand binding and the neglected dynamics of the protein-ligand complex in current scoring schemes. We have developed a new methodology, named the 'ligand-model' concept, to sample protein conformations that are relevant for binding structurally diverse sets of ligands. In the ligand-model concept, molecular-dynamics (MD) simulations are performed with a virtual ligand, represented by a collection of functional groups that binds to the protein and dynamically changes its shape and prope

SUBMITTER: Xu M 

PROVIDER: S-EPMC3172320 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature