Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield

Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we (Bhadra and Pal, 2014; Proteins: Structure, Function, and Bioinformatics 82: 2443 –2454; DOI: 10.1002/prot.24609) developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory.

Source: Computers in Biology and Medicine - February 22, 2017 Category: Bioinformatics Authors: Pratiti Bhadra, Debnath Pal Source Type: research