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相关概念视频

Protein Folding01:25

Protein Folding

8.1K
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...
8.1K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.7K
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

18.0K
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...
18.0K
Protein and Protein Structure02:15

Protein and Protein Structure

79.7K
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...
79.7K
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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相关实验视频

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-Fold3:一个基于梯度的蛋白质全原子折叠和对接框架在TensorFlow上.

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
概括
此摘要是机器生成的。

OPUS-Fold3是一个新的AI框架,用于蛋白质结构生成. 它准确地建模了蛋白质折叠和对接,在侧链建模中表现优于现有的工具.

关键词:
低温电磁密度地图蛋白质对接框架 蛋白质对接框架蛋白质折叠框架 蛋白质折叠框架

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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05:08

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

  • 计算生物学 计算生物学
  • 结构生物信息学 结构生物信息学
  • 人工智能在生物学中的应用

背景情况:

  • 准确的蛋白质结构预测对于分子设计和功能分析至关重要.
  • 现有的蛋白质折叠和对接框架在效率和准确性方面存在局限性,特别是在复杂的建模任务中.

研究的目的:

  • 介绍OPUS-Fold3,一种基于梯度的全原子框架,用于蛋白质折叠和对接.
  • 为了证明框架在特定约束下生成准确的3D蛋白质结构的能力.
  • 为科学界提供一个易于使用和适应的工具.

主要方法:

  • 使用 Python 和 TensorFlow 2.4.4 开发 OPUS-Fold3 的开发.
  • 实现基于梯度的全原子方法用于蛋白质结构建模.
  • 基于约束的结构生成,利用取决于重原子位置的潜在函数.

主要成果:

  • 在骨干折叠中,OPUS-Fold3表现出与pyRosetta相当的性能.
  • 与pyRosetta.com相比,该框架在侧链建模方面表现明显优越.
  • 成功生成符合用户定义约束的3D蛋白质结构.

结论:

  • OPUS-Fold3为蛋白质折叠和对接提供了一种高效准确的解决方案.
  • 该框架的灵活性促进了与其他深度学习模型的整合,促进了跨学科的研究.
  • OPUS-Fold3可以免费用于学术用途,促进结构生物学和人工智能的进步.