한빛사 논문
Gyu Rie Lee†, Jonghun Won†, Lim Heo and Chaok Seok*
Department of Chemistry, Seoul National University, Seoul 08826, Korea
*To whom correspondence should be addressed.
Present addresses: Gyu Rie Lee, Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Lim Heo, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
†The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.
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.
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