Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach

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Title
Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach
Author(s)
T R Kim; J S Yang; S Shin; Jinhyuk Lee
Bibliographic Citation
Proteins-Structure Function and Bioinformatics, vol. 81, no. 7, pp. 1156-1165
Publication Year
2013
Abstract
A set of grid type knowledge-based energy functions is introduced for φ{symbol}-χ1, ψ-χ1, φ{symbol}-ψ, and χ1-χ2 torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X-ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement.
Keyword
Bicubic interpolationStatistical potentialStructure modelingTorsion angle
ISSN
0887-3585
Publisher
Wiley
DOI
http://dx.doi.org/10.1002/prot.24265
Type
Article
Appears in Collections:
Division of Biomedical Research > Disease Target Structure Research Center > 1. Journal Articles
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