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Related Concept Videos

Protein Folding01:25

Protein Folding

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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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Protein and Protein Structure02:15

Protein and Protein Structure

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
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Protein and Protein Structures02:15

Protein and Protein Structures

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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Related Experiment Video

Updated: Jul 13, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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OPUS-Fold3: a gradient-based protein all-atom folding and docking framework on TensorFlow.

Gang Xu1,2,3, Zhenwei Luo1,2,3, Ruhong Zhou4,5

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

Briefings in Bioinformatics
|October 14, 2023
PubMed
Summary
This summary is machine-generated.

OPUS-Fold3 is a new AI framework for protein structure generation. It accurately models protein folding and docking, outperforming existing tools in side-chain modeling.

Keywords:
cryo-EM density mapprotein docking frameworkprotein folding framework

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Artificial Intelligence in Biology

Background:

  • Accurate protein structure prediction is crucial for molecular design and function analysis.
  • Existing protein folding and docking frameworks face limitations in efficiency and accuracy, particularly for complex modeling tasks.

Purpose of the Study:

  • To introduce OPUS-Fold3, a novel gradient-based, all-atom framework for protein folding and docking.
  • To demonstrate the framework's capability in generating accurate 3D protein structures under specified constraints.
  • To provide a user-friendly and adaptable tool for the scientific community.

Main Methods:

  • Development of OPUS-Fold3 using Python and TensorFlow 2.4.
  • Implementation of a gradient-based, all-atom approach for protein structure modeling.
  • Constraint-based structure generation utilizing potential functions dependent on heavy atom positions.

Main Results:

  • OPUS-Fold3 demonstrates performance comparable to pyRosetta in backbone folding.
  • The framework shows significantly superior performance in side-chain modeling compared to pyRosetta.
  • Successful generation of 3D protein structures compliant with user-defined constraints.

Conclusions:

  • OPUS-Fold3 offers an efficient and accurate solution for protein folding and docking.
  • The framework's flexibility facilitates integration with other deep learning models, fostering interdisciplinary research.
  • OPUS-Fold3 is freely available for academic use, promoting advancements in structural biology and AI.