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OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding.


ABSTRACT:

Motivation

The development of an open-source platform to predict protein 1D features and 3D structure is an important task. In this paper, we report an open-source toolkit for protein 3D structure modeling, named OPUS-X. It contains three modules: OPUS-TASS2, which predicts protein torsion angles, secondary structure and solvent accessibility; OPUS-Contact, which measures the distance and orientation information between different residue pairs; and OPUS-Fold2, which uses the constraints derived from the first two modules to guide folding.

Results

OPUS-TASS2 is an upgraded version of our previous method OPUS-TASS. OPUS-TASS2 integrates protein global structure information and significantly outperforms OPUS-TASS. OPUS-Contact combines multiple raw co-evolutionary features with protein 1D features predicted by OPUS-TASS2, and delivers better results than the open-source state-of-the-art method trRosetta. OPUS-Fold2 is a complementary version of our previous method OPUS-Fold. OPUS-Fold2 is a gradient-based protein folding framework based on the differentiable energy terms in opposed to OPUS-Fold that is a sampling-based method used to deal with the non-differentiable terms. OPUS-Fold2 exhibits comparable performance to the Rosetta folding protocol in trRosetta when using identical inputs. OPUS-Fold2 is written in Python and TensorFlow2.4, which is user-friendly to any source-code-level modification.

Availabilityand implementation

The code and pre-trained models of OPUS-X can be downloaded from https://github.com/OPUS-MaLab/opus_x.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Xu G 

PROVIDER: S-EPMC8696105 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Publications

OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding.

Xu Gang G   Wang Qinghua Q   Ma Jianpeng J  

Bioinformatics (Oxford, England) 20211201 1


<h4>Motivation</h4>The development of an open-source platform to predict protein 1D features and 3D structure is an important task. In this paper, we report an open-source toolkit for protein 3D structure modeling, named OPUS-X. It contains three modules: OPUS-TASS2, which predicts protein torsion angles, secondary structure and solvent accessibility; OPUS-Contact, which measures the distance and orientation information between different residue pairs; and OPUS-Fold2, which uses the constraints  ...[more]

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