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• W2020122119 startingPage "2568" @default.
• W2020122119 abstract "Protein structure prediction (PSP) is a long standing problem in structural biology and bioinformatics. Within the PSP problem loop refinement is a major bottleneck. In this article we report the latest version of the CReF expert predictor system for the PSP problem with emphasis on loop refinement of the approximate 3-D structure 1ZDD_P of the Z34C mini protein predicted by CReF. We designed a loop refinement protocol based on seven molecular dynamics (MD) simulations runs at different temperatures. We found that, by letting the loop residues move freely during dynamics at 325 K and restraining the internal coordinates of the correctly predicted helical structures, while allowing them to move relative to each other, the refinement protocol was very effective in predicting an accurate loop conformation in the first 100 ps of a 1000 ps MD simulation. The quality of the predictions was confirmed by the RMSD between refined and experimental structures which varied from 0.6 to 1.3 Å. In addition, stereochemical analyses showed that 100% of all residues of the refined 1ZDD_P, including those in the loop, populates the most favorable core regions of the Ramachandran plot. Our study suggests that the proposed protocol may be suitable to refine more complex mini proteins with different classes and architectures." @default.
• W2020122119 created "2016-06-24" @default.
• W2020122119 creator A5064713906 @default.
• W2020122119 creator A5070327657 @default.
• W2020122119 date "2013-06-01" @default.
• W2020122119 modified "2023-09-27" @default.
• W2020122119 title "An expert protein loop refinement protocol by molecular dynamics simulations with restraints" @default.
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• W2020122119 doi "https://doi.org/10.1016/j.eswa.2012.10.062" @default.
• W2020122119 hasPublicationYear "2013" @default.
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