Paper Citing NAMD - Abstract
Patel, Jagdish Suresh; Branduardi, Davide; Masetti, Matteo; Rocchia, Walter; Cavalli, Andrea
Insights into Ligand-Protein Binding from Local Mechanical Response
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3368-3378, OCT 2011
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)-roscovitine/CDKS complex). Then, we devised a novel postprocessing tool to be applied to the local mechanical responses, to extract structural information related to the biological processes under investigation. Despite the out-of-equilibrium character of the trajectories, the analysis carried out on the work profiles provided pivotal information about the investigated biological processes. This could eventually be applied to drug design.
