Introduction

Protein structures predicted by state-of-the-art template-based methods may still have errors when the template proteins are not similar enough to the target protein. Overall target structure may deviate from the template structures owing to differences in sequences. Structural information for some local regions such as loops may not be available when there are sequence insertions or deletions. Those structural aspects that originate from deviations from templates can be dealt with by ab initio structure refinement methods to further improve model accuracy. In the CASP11 refinement experiment, we tested three different refinement methods that utilize overall structure relaxation, loop modeling, and quality assessment of multiple initial structures. From this experiment, we conclude that the overall relaxation method can consistently improve model quality. Loop modeling is the most useful when the initial model structure is high quality, with GDT-HA >60. The method that used multiple initial structures further refined the already refined models; the minor improvements with this method raise the issue of problem with the current energy function. Future research directions are also discussed. Proteins 2016; 84(Suppl 1):293-301. © 2015 Wiley Periodicals, Inc.

Publications

  1. Effective protein model structure refinement by loop modeling and overall relaxation.
    Cite this
    Lee GR, Heo L, Seok C, 2016-09-01 - Proteins
  2. GalaxyRefine: Protein structure refinement driven by side-chain repacking.
    Cite this
    Heo L, Park H, Seok C, 2013-07-01 - Nucleic acids research

Credits

  1. Gyu Rie Lee
    Developer

    Department of Chemistry, Seoul National University

  2. Lim Heo
    Developer

    Department of Chemistry, Seoul National University

  3. Chaok Seok
    Investigator

    Department of Chemistry, Seoul National University

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Summary
AccessionBT006393
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
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Submitted ByChaok Seok