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.

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call

Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.