Published on Tue Jun 22 2021

ROPIUS0: A deep learning-based protocol for protein structure prediction and model selection and its performance in CASP14

Margelevicius, M.

A protocol ROPIUS0 for protein structure prediction and model selection is presented. It is shown that the direct use of predicted inter-residue distances may be sufficient to discriminate between correct and incorrect protein folds.

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Abstract

A protocol ROPIUS0 for protein structure prediction and model selection is presented. At the core of the ROPIUS0 protocol is the deep learning module developed for the selection of protein structural models. It is shown that the direct use of predicted inter-residue distances may be sufficient to discriminate between correct and incorrect protein folds, considering only a small fraction of predicted distances. Having finished the latest CASP14 prediction season, a ROPIUS0 variant based on model selection ranks 13th in the category of tertiary structure prediction. Its performance is on par with top-performing automated prediction servers when tested on the CASP13 dataset. The results suggest ways to improve searching for structurally similar and homologous proteins without considerably increasing speed.