Dataset Information

OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.

ABSTRACT: 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.

SUBMITTER: Xu G

PROVIDER: S-EPMC6193766 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.

Xu Gang G Ma Tianqi T Zang Tianwu T Sun Weitao W Wang Qinghua Q Ma Jianpeng J

Journal of molecular biology 20170831 20

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 tra ...[more]

PMID: 28864201

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Project description:Significant advancements in the field of protein structure prediction have necessitated the need for objective and robust evaluation of protein structural models by comparing predicted models against the experimentally determined native structures to quantitate their structural similarities. Existing protein model versus native similarity metrics either consider the distances between alpha carbon (C?) or side-chain atoms for computing the similarity. However, side-chain orientation of a protein plays a critical role in defining its conformation at the atomic-level. Despite its importance, inclusion of side-chain orientation in structural similarity evaluation has not yet been addressed. Here, we present SPECS, a side-chain-orientation-included protein model-native similarity metric for improved evaluation of protein structural models. SPECS combines side-chain orientation and global distance based measures in an integrated framework using the united-residue model of polypeptide conformation for computing model-native similarity. Experimental results demonstrate that SPECS is a reliable measure for evaluating structural similarity at the global level including and beyond the accuracy of C? positioning. Moreover, SPECS delivers superior performance in capturing local quality aspect compared to popular global C? positioning-based metrics ranging from models at near-experimental accuracies to models with correct overall folds-making it a robust measure suitable for both high- and moderate-resolution models. Finally, SPECS is sensitive to minute variations in side-chain ? angles even for models with perfect C? trace, revealing the power of including side-chain orientation. Collectively, SPECS is a versatile evaluation metric covering a wide spectrum of protein modeling scenarios and simultaneously captures complementary aspects of structural similarities at multiple levels of granularities. SPECS is freely available at http://watson.cse.eng.auburn.edu/SPECS/.

Dataset Information

OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.

Publications

OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.

Similar Datasets

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