Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging
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Updated: May 10, 2026
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Vahid Mirjalili1, Keenan Noyes, Michael Feig
1Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan, 48824; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824.
Abstract:
We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD-based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail.
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