OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation-Reference-Cited by-同舟云学术

OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation

Published:2020-01-14 Issue:2 Volume:16 Page:1359-1366
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Xu Gang¹,Wang Qinghua²,Ma Jianpeng¹²³^ORCID

Affiliation:

1. Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China

2. Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030, United States

3. Department of Bioengineering, Rice University, Houston, Texas 77005, United States

Funder

Gillson Longenbaugh Foundation

Welch Foundation

Science and Technology Commission of Shanghai Municipality

U.S. Department of Health and Human Services

National Basic Research Program of China

ZJLab

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.9b01054

Reference33 articles.

1. End-to-End Differentiable Learning of Protein Structure

2. Protein Structure Prediction Using Rosetta

3. I-TASSER: a unified platform for automated protein structure and function prediction

4. Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility

5. ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction

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1. IGPRED-MultiTask: A Deep Learning Model to Predict Protein Secondary Structure, Torsion Angles and Solvent Accessibility;IEEE/ACM Transactions on Computational Biology and Bioinformatics;2023-03-01

2. OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods;Journal of Chemical Information and Modeling;2020-11-19

3. OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks;Bioinformatics;2020-07-17

4. OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling;Journal of Chemical Theory and Computation;2020-04-23