Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jul;41(Web Server issue):W384-8.
doi: 10.1093/nar/gkt458. Epub 2013 Jun 3.

GalaxyRefine: Protein structure refinement driven by side-chain repacking

Lim Heo  1 , Hahnbeom Park, Chaok Seok
Affiliations

GalaxyRefine: Protein structure refinement driven by side-chain repacking

Lim Heo et al. Nucleic Acids Res. 2013 Jul.

Abstract

The quality of model structures generated by contemporary protein structure prediction methods strongly depends on the degree of similarity between the target and available template structures. Therefore, the importance of improving template-based model structures beyond the accuracy available from template information has been emphasized in the structure prediction community. The GalaxyRefine web server, freely available at http://galaxy.seoklab.org/refine, is based on a refinement method that has been successfully tested in CASP10. The method first rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. According to the CASP10 assessment, this method showed the best performance in improving the local structure quality. The method can improve both global and local structure quality on average, when used for refining the models generated by state-of-the-art protein structure prediction servers.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Refinement results for a CASP10 target TR681. (A) The initial structure (pink, GDT-HA = 57.6) and (B) the refined structure (cyan, GDT-HA = 64.1) is shown superimposed to the experimental structure (brown). Multi-criterion kinemage of (C) the initial structure (MolProbity score = 2.90) and (D) the refined structure (MolProbity score = 2.06). MolProbity highlights steric clashes as pink spikes, poor rotamers as gold side-chains and Ramachandran outliers as green lines.
Figure 2.
Figure 2.
GalaxyRefine output page. The five top-ranking models are shown in static images, and they can also be viewed using the Jmol structure viewer. The structure changes relative to the initial model in terms of GDT-HA, RMSD and MolProbity score are presented in a separate table. Three components of the MolProbity score, namely, the number of atomic clashes per 1000 atoms, the percentages of rotamer outliers and Ramachandran favored backbone torsion angles, are also reported in the table.
See this image and copyright information in PMC

References

    1. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000;29:291–325. - PubMed
    1. Kryshtafovych A, Fidelis K, Moult J. CASP9 results compared to those of previous CASP experiments. Proteins. 2011;79(Suppl. 10):196–207. - PMC - PubMed
    1. Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y. Assessment of CASP8 structure predictions for template free targets. Proteins. 2009;77(Suppl. 9):50–65. - PubMed
    1. Kinch L, Yong Shi S, Cong Q, Cheng H, Liao Y, Grishin NV. CASP9 assessment of free modeling target predictions. Proteins. 2011;79(Suppl. 10):59–73. - PMC - PubMed
    1. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009;77(Suppl. 9):66–80. - PMC - PubMed

Publication types