Statistical torsion angle potential energy functions for protein structure modeling: A bicubic interpolation approach |
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Authors: | Tae‐Rae Kim Joshua SungWoo Yang Seokmin Shin Jinhyuk Lee |
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Affiliation: | 1. Department of Chemistry, Seoul National University, , Seoul 151‐747, Republic of Korea;2. Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, , Yuseong‐gu, Daejeon 305‐806, Republic of Korea;3. Department of Bioinformatics, University of Science and Technology, , Yuseong‐Gu, Daejeon 305‐350, Republic of Korea |
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Abstract: | A set of grid type knowledge‐based energy functions is introduced for ?–χ1, ψ–χ1, ?–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. Proteins 2013. Proteins 2013; 81:1156–1165. © 2013 Wiley Periodicals, Inc. |
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Keywords: | torsion angle statistical potential structure modeling bicubic interpolation |
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