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相关概念视频

Protein-protein Interfaces02:04

Protein-protein Interfaces

13.3K
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...
13.3K
Ligand Binding Sites02:40

Ligand Binding Sites

13.2K
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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Conserved Binding Sites01:49

Conserved Binding Sites

4.4K
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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Improving Translational Accuracy02:07

Improving Translational Accuracy

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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 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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相关实验视频

Updated: Sep 13, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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一个对比平台,用于评估蛋白质语言模型对功能相关预测任务的评估.

Elif Çevrim1,2, Melih Gökay Yiğit1,3, Erva Ulusoy1,2

  • 1Biological Data Science Lab, Department of Computer Engineering, Hacettepe University, Ankara, Turkey.

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概括

我们介绍了PROBE,这是一个新的工具,用于对蛋白质表示进行基准测试,以预测功能. PROBE评估经典方法和蛋白质语言模型 (PLM),帮助研究人员选择最佳方法来获得生物学见解.

关键词:
基准测试框架 基准测试框架基因本体学是基因的本体学.蛋白质家族是一个蛋白质家族.蛋白质功能的预测和预测蛋白质语言模型的模型蛋白质蛋白质相互作用代表性的学习学习.

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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相关实验视频

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科学领域:

  • 生物化学和分子生物学
  • 生物信息学和计算生物学

背景情况:

  • 蛋白质对生物过程至关重要,为科学进步和生物技术创新需要准确的功能注释.
  • 传统的基于同质学的方法和新兴的机器学习 (ML) 方法,特别是蛋白质语言模型 (PLM),是预测蛋白质功能的关键.
  • PLM擅长通过专门的深度学习架构捕捉复杂的序列结构功能关系.

研究的目的:

  • 引入蛋白质表示基准 (PROBE),用于评估功能预测任务中的蛋白质表示的框架.
  • 通过GitHub和Web服务提供使用PROBE框架的详细协议.
  • 通过评估既有和新型的多式联运 PLM 来证明 PROBE 的实用性.

主要方法:

  • 开发了PROBE基准测试框架,其核心任务有四项:语义相似性推断,基于本体学的功能预测,药物向家族分类和蛋白质-蛋白质结合亲缘关系估计.
  • 实施一个用户友好的Web服务和一个GitHub存储库,以实现PROBE可访问性.
  • 蛋白质表示的评估,包括经典方法和PLM如ESM2,ESM3,ProstT5和SaProt,使用不同的数据类型 (序列和结构).

主要成果:

  • PROBE有效地对各种蛋白质表示进行基准测试,包括经典方法和先进的PLM.
  • 多模式PLM在整合序列和结构信息以提高功能预测方面表现出能力.
  • 这项研究强调了PLM在提高蛋白质功能预测准确性和实用性的潜力.

结论:

  • PROBE工具提供了一个标准化的框架来评估蛋白质表征,这对于促进生物学理解至关重要.
  • 蛋白质语言模型显示了改善蛋白质功能预测的显著前景,使模型开发人员和最终用户都受益.
  • PROBE促进了对蛋白质表示方法的明智选择,加速了生物技术和治疗学的研究.