ArticleProtein science : a publication of the Protein Society2019
OPUS-SSF: A side-chain-inclusive scoring function for ranking protein structural models.
Article in Protein science : a publication of the Protein Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation.Biophysical journal · 2022Article
- A simple neural network implementation of generalized solvation free energy for assessment of protein structural models.RSC advances · 2019Article
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4 authors.
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Abstract
We introduce a side-chain-inclusive scoring function, named OPUS-SSF, for ranking protein structural models. The method builds a scoring function based on the native distributions of the coordinate components of certain anchoring points in a local molecular system for peptide segments of 5, 7, 9, and 11 residues in length. Differing from our previous OPUS-CSF [Xu et al., Protein Sci. 2018; 27: 286-292], which exclusively uses main chain information, OPUS-SSF employs anchoring points on side chains so that the effect of side chains is taken into account. The performance of OPUS-SSF was tested on 15 decoy sets containing totally 603 proteins, and 571 of them had their native structures recognized from their decoys. Similar to OPUS-CSF, OPUS-SSF does not employ the Boltzmann formula in constructing scoring functions. The results indicate that OPUS-SSF has achieved a significant improvement on decoy recognition and it should be a very useful tool for protein structural prediction and modeling.
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