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
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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