Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 429, Issue 20, Pages 3113-3120Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2017.08.013
Keywords
protein structure prediction; empirical potential function; protein folding; decoy recognition; side-chain packing
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Funding
- National Institutes of Health [R01-GM067801, R01-GM116280, R01-AI067839]
- Welch Foundation [Q-1512, Q-1826]
- Gillson-Longenbaugh Foundation
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We report a new distance- and orientation-dependent, all-atom statistical potential derived from side-chain packing, named OPUS-DOSP, for protein structure modeling. The framework of OPUS-DOSP is based on OPUS-PSP, previously developed by us [JMB (2008), 376, 288-301], with refinement and new features. In particular, distance or orientation contribution is considered depending on the range of contact distance. A new auxiliary function in energy function is also introduced, in addition to the traditional Boltzmann term, in order to adjust the contributions of extreme cases. OPUS-DOSP was tested on 11 decoy sets commonly used for statistical potential benchmarking. Among 278 native structures, 239 and 249 native structures were recognized by OPUS-DOSP without and with the auxiliary function, respectively. The results show that OPUS-DOSP has an increased decoy recognition capability comparing with those of other relevant potentials to date. (C) 2017 Published by Elsevier Ltd.
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