ArticleJournal of molecular biology2017
OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.
Article in Journal of molecular biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information.Molecules (Basel, Switzerland) · 2025Article
- OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors.Briefings in bioinformatics · 2022Article
- Secondary structure specific simpler prediction models for protein backbone angles.BMC bioinformatics · 2022Article
- Article
- Enhancing protein backbone angle prediction by using simpler models of deep neural networks.Scientific reports · 2020Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- A simple neural network implementation of generalized solvation free energy for assessment of protein structural models.RSC advances · 2019Article
- OPUS-SSF: A side-chain-inclusive scoring function for ranking protein structural models.Protein science : a publication of the Protein Society · 2019Article
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Authors and funding
6 authors.
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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.
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