Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD

A method for the local refinement of protein structures that targets improvements in local stereochemistry while preserving the overall fold is presented. The method uses force field-based minimization and sampling via molecular dynamics simulations with a modified force field to bring bonds, angles, and torsion angles into an acceptable range for high-resolution protein structures. The method is implemented in the locPREFMD web server and was tested on computational models submitted to CASP11. Using MolProbity scores as the main assessment criterion, the locPREFMD method significantly improves the stereochemical quality of given input models close to the quality expected for experimental structures while maintaining the Ca coordinates of the initial model.