FG-MD is a molecular dynamics (MD) based algorithm for atomic-level protein structure refinement. Given an initial protein structure, FG-MD first identifies analogous fragments from the PDB by the structural alignment program TM-align. Spatial restraints extracted from the fragments are then used to to re-shape the funnel of the MD energy landscape and guide the MD conformational sampling. FG-MD aims to refine the initial models closer to the native structure. It can also improve the local geometry of the structures by removing the steric clashes and improving the torsion angle and the hydrogen-binding networks.
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Proteins. 2011;79 Suppl 10:147-60. doi: 10.1002/prot.23111. Epub 2011 Aug 23.
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.
Xu D1, Zhang J, Roy A, Zhang Y.