GalaxyWEB server for protein structure prediction and refinement
By Junsu Ko, Hahnbeom Park, Lim Heo, Chaok Seok. Nucleic Acids Res., 2012
905 citations recorded by the source corpus.
Three-dimensional protein structures provide invaluable information for understanding and regulating biological functions of proteins. The GalaxyWEB server predicts protein structure from sequence by template-based modeling and refines loop or terminus regions by ab initio modeling. This web server is based on the method tested in CASP9 (9th Critical Assessment of techniques for protein Structure Prediction) as ‘Seok-server’, which was assessed to be among top performing template-based modeling servers. The method generates reliable core structures from multiple templates and re-builds unreliable loops or termini by using an optimization-based refinement method. In addition to structure prediction, a user can also submit a refinement only job by providing a starting model structure and locations of loops or termini to refine. The web server can be freely accessed at http://galaxy.seoklab.org/.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3c4b79359ed2e70c5bd59342e61d222c085a8a48
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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): “The GalaxyRefine web server for protein structure refinement (8) was released on the GalaxyWEB server (9,10) in 2013.”
- Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “55,83,181,187 It will require additional efforts and resources to focus on optimizing computational ef fi ciency for MD-based methods so that more signi fi cant re fi nement via web-based services can bene fi t the broader community.”