GalaxyRefine: protein structure refinement driven by side-chain repacking

By Lim Heo, Hahnbeom Park, Chaok Seok. Nucleic Acids Res., 2013

1,217 citations recorded by the source corpus.

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.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/3cde40ce8a488bc4ff7c97fc2449eda10660f32e

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Citations in the corpus

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization (2015, methodology): “Of the model structures generated by GalaxyTBM, 10 structures are selected by choosing the structures with the best energy values for each template and are further refined following the GalaxyRefine (21) protocol.”
GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure (2019, methodology): “Here, we present GalaxyRefine2, an upgraded version of GalaxyRefine (8), which reflects a progress made during recent CASP experiments (18).”
Driven to Near-Experimental Accuracy by Refinement via Molecular Dynamics Simulations (2019, background): “GalaxyRefine sampled structures by perturbing conformations in various ways focusing on rearranging side chains, secondary structure elements, or even more global structural changes in order to cross energy barriers believed to hinder refinement.(13,22) However, these strategies were not successful ”
3Drefine: an interactive web server for efficient protein structure refinement (2016, methodology): “The biggest advantage of i3Drefine method compared to other state-of-the-art refinement methods like KobaMin (21) and GalaxyRefine (22) is consistency.”
ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates (2017, methodology): “This means that MDS refinement protocols, such as those developed by the Feig group, would be less practical to be used routinely for large scale fully automated structure prediction pipelines.”
In silico SARS-CoV-2 vaccine development for Omicron strain using reverse vaccinology (2022, methodology): “org/) server was used to refine and relax the protein construct (Heo et al. 2013).”