Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

Authors

  • Vahid Mirjalili,

    1. Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan
    2. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
    Search for more papers by this author
  • Keenan Noyes,

    1. Department of Chemistry, Michigan State University, East Lansing, Michigan
    Search for more papers by this author
  • Michael Feig

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
    2. Department of Chemistry, Michigan State University, East Lansing, Michigan
    • Correspondence to: Michael Feig, Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, 218 BCH, East Lansing, MI 48824. E-mail: feig@msu.edu

    Search for more papers by this author

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. Proteins 2014; 82(Suppl 2):196–207. © 2013 Wiley Periodicals, Inc.

Ancillary