GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

By Gyu Rie Lee, Jonghun Won, Lim Heo, Chaok Seok. 2019

128 citations recorded by the source corpus.

Abstract The 3D structure of a protein can be predicted from its amino acid sequence with high accuracy for a large fraction of cases because of the availability of large quantities of experimental data and the advance of computational algorithms. Recently, deep learning methods exploiting the coevolution information obtained by comparing related protein sequences have been successfully used to generate highly accurate model structures even in the absence of template structure information. However, structures predicted based on either template structures or related sequences require further improvement in regions for which information is missing. Refining a predicted protein structure with insufficient information on certain regions is critical because these regions may be connected to functional specificity that is not conserved among related proteins. The GalaxyRefine2 web server, freely available via http://galaxy.seoklab.org/refine2, is an upgraded version of the GalaxyRefine protein structure refinement server and reflects recent developments successfully tested through CASP blind prediction experiments. This method adopts an iterative optimization approach involving various structure move sets to refine both local and global structures. The estimation of local error and hybridization of available homolog structures are also employed for effective conformation search.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIII (2019, background): “These range from a major focus on molecular dynamics(28) to hybrid Monte Carlo/sampling methods,(29) to methods dominated by sampling.(30) But overall, there is an increasing emphasis on the importance of conformational sampling.”