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相关概念视频

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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Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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重温蛋白质-蛋白质对接:一个系统的评估框架.

Linlong Jiang1,2, Ke Zhang2,3, Kai Zhu1,2

  • 1College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.

Journal of chemical information and modeling
|September 18, 2025
PubMed
概括
此摘要是机器生成的。

一个新的框架对蛋白质-蛋白质对接方法进行了基准测试. AlphaFold3在预测复杂结构方面表现出色,优于传统工具,但深度学习模型在分布外概括方面扎.

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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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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物学是结构生物学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 蛋白质与蛋白质之间的相互作用对于生物过程至关重要.
  • 精确预测蛋白质复杂结构对于理解机制和药物设计至关重要.
  • 蛋白质-蛋白质对接方法需要严格的评估.

研究的目的:

  • 为评估蛋白质-蛋白质对接方法建立一个全面的基准测试框架.
  • 为了比较传统和基于深度学习 (DL) 的对接方法.
  • 评估DL模型的分发外 (OOD) 泛化能力.

主要方法:

  • 使用DockingBenchmark 5.5,AACBench和PPCBench数据集开发了一个基准测试框架.
  • 评估了11种对接方法,包括传统的 (HDOCK,PatchDock,PIPER,ZDOCK) 和基于DL的 (AlphaFold3,AlphaFold-Multimer等). ) 的情况.
  • 评估了灵活对接,抗体-抗原复合对接和OOD概括的性能.

主要成果:

  • 在对抗apo结构时,AlphaFold3表现出优越的前5名成功率 (77.98%) .
  • 在对抗全息结构时,HDOCK的成功率很高 (85.24%),但对抗阿波的成功率较低.
  • 在抗体-抗原对接方面,AlphaFold3是最准确的 (31.78%的成功率),并且表现优于AlphaFold-Multimer.
  • 所有DL模型都在OOD PPCBench数据集上显示性能降低.

结论:

  • 拟议的框架允许对各种蛋白质-蛋白质对接方法进行系统评估.
  • AlphaFold3表现出强大的性能,特别是在对抗阿波结构和抗体-抗原建模中.
  • 目前基于DL的对接方法在OOD泛化方面面临挑战,突出了未来改进的领域.