Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method.

ABSTRACT: The challenge in protein structure prediction using homology modeling is the lack of reliable methods to refine the low resolution homology models. Unconstrained all-atom molecular dynamics (MD) does not serve well for structure refinement due to its limited conformational search. We have developed and tested the constrained MD method, based on the generalized Newton-Euler inverse mass operator (GNEIMO) algorithm for protein structure refinement. In this method, the high-frequency degrees of freedom are replaced with hard holonomic constraints and a protein is modeled as a collection of rigid body clusters connected by flexible torsional hinges. This allows larger integration time steps and enhances the conformational search space. In this work, we have demonstrated the use of torsional GN

SUBMITTER: Park IH 

PROVIDER: S-EPMC3377353 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature