Insights into Ligand-Protein Binding from Local Mechanical Response.

ABSTRACT: Computational studies of ligand-protein binding are crucial for properly designing novel compounds of potential pharmacological interest. In this respect, researchers are increasingly interested in steered molecular dynamics for ligand-protein binding and unbinding studies. In particular, it has been suggested that analyzing the work profiles along the ligand-protein undocking paths could be fruitful. Here, we propose that small portions of work profiles, termed "local mechanical responses" of the system to a steering force, could serve as a universal measure for capturing relevant information about the system under investigation. Specifically, we first collected a high number of steering trajectories using two biological systems of increasing complexity (i.e., alanine dipeptide and (R)-ro

SUBMITTER: Patel JS 

PROVIDER: S-EPMC3191767 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature