An example of structure refinement by FG-MD (Fragment-Guided Molecular Dynamics simulation) for TR614, the pleckstrin homology domain of Saccharomyces cerevisiae Avo1, a structure refinement target in CASP9 (the 9th Critical Assessment of protein Structure Prediction experiment). The initial structure is among the best models selected by the organizer from the CASP9 server predictions. Segment structures searched by TM-align were used to reshape the MD energy landscape, which resulted in a TM-score increase by 9 units. (a) Superposition of the initial model (green), the refined model (blue) and the native structure (red). (b) A plot of energy versus TM-score for a set of 77×220 refined models generated by the conventional molecular dynamic simulation program AMBER99 (black circles) and FG-MD (red squares), respectively, starting from 77 decoy models of different resolutions. The curves are connection of the medians of the ten lowest-energy models in each of the TM-score bins, where a funnel-like shape appears in the energy landscape of the FG-MD simulations but is absent from that of the AMBER99 simulations.
Zhang and Skolnick BMC Biology 2013 11:44 doi:10.1186/1741-7007-11-44