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OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling.

Journal of chemical theory and computation·2023
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OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding.

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OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods.

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

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OPUS-Rota2: An Improved Fast and Accurate Side-Chain Modeling Method.

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OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling.

Gang Xu1, Qinghua Wang2, Jianpeng Ma1,2,3

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

Journal of Chemical Theory and Computation
|April 24, 2020
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Summary
This summary is machine-generated.

OPUS-Fold is a novel protein folding framework that integrates diverse methods for accurate and efficient protein structure prediction. It balances speed and accuracy, enabling the incorporation of various subproblem solutions, including experimental data.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein structure prediction is crucial for understanding biological function.
  • Integrating diverse computational methods remains a challenge in protein folding.

Purpose of the Study:

  • To introduce OPUS-Fold, a flexible protein folding framework.
  • To facilitate the integration of various subproblem methods for enhanced protein structure prediction.

Main Methods:

  • Torsion-angle sampling for protein backbone generation.
  • A multi-term energy function for model quality estimation.
  • Incorporation of OPUS-Rota2 for fast side-chain modeling.

Main Results:

  • OPUS-Fold balances accuracy and efficiency in protein folding.
  • The framework allows for the integration of various subproblem methods.
  • Enables the use of all-atom models and nondifferentiable data.

Conclusions:

  • OPUS-Fold provides a versatile platform for protein folding.
  • It supports the incorporation of diverse computational and experimental data.
  • The framework is available as open-source software.