Jove
Visualize
联系我们
JoVE
x logofacebook logolinkedin logoyoutube logo
关于 JoVE
概览领导团队博客JoVE 帮助中心
作者
出版流程编辑委员会范围与政策同行评审常见问题投稿
图书馆员
用户评价订阅访问资源图书馆顾问委员会常见问题
研究
JoVE JournalMethods CollectionsJoVE Encyclopedia of Experiments存档
教育
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab Manual教师资源中心教师网站
使用条款与条件
隐私政策
政策

相关概念视频

Conserved Binding Sites01:49

Conserved Binding Sites

5.0K
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...
5.0K
Conserved Binding Sites01:49

Conserved Binding Sites

1.9K
1.9K
Ligand Binding Sites02:40

Ligand Binding Sites

14.8K
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...
14.8K
Ligand Binding Sites02:40

Ligand Binding Sites

8.5K
8.5K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.4K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.4K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.4K
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...
14.4K

您也可能阅读

相关文章

通过共同作者、期刊和引用图与本文相关的文章。

排序
Same author

Polypharmacology is an enduring and nearly universal property of kinase inhibitors.

bioRxiv : the preprint server for biology·2026
Same author

Viral escape-inspired framework for structure-guided dual bait protein biosensor design.

PLoS computational biology·2025
Same author

Fermi calculations enable quick downselection of target genes and process optimization in photosynthetic systems.

Plant physiology·2025
Same author

Robust Prediction of Enzyme Variant Kinetics with RealKcat.

bioRxiv : the preprint server for biology·2025
Same author

Exploring putative enteric methanogenesis inhibitors using molecular simulations and a graph neural network.

bioRxiv : the preprint server for biology·2024
Same author

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass.

Journal of experimental botany·2023

相关实验视频

Updated: Jan 10, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.7K

Seq2Bind网络服务器用于使用微调的蛋白质语言模型从序列中预测绑定位点.

Xiang Ma1,2, Supantha Dey3, Vaishnavey Sr3

  • 1Department of Computer Science, Iowa State University, Ames, IA 50011, United States.

NAR genomics and bioinformatics
|November 24, 2025
PubMed
概括

Seq2Bind使用蛋白质语言模型来预测蛋白质结合部位和仅从序列的亲和力. 这种计算工具有助于通过快速选蛋白相互作用来识别治疗点.

更多相关视频

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.5K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.1K

相关实验视频

Last Updated: Jan 10, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.7K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.5K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

7.1K

科学领域:

  • 计算生物学 计算生物学
  • 结构生物学 结构生物学
  • 药物发现 药物发现 药物发现

背景情况:

  • 蛋白与蛋白相互作用 (PPI) 是细胞过程的基础.
  • 在残留水平上了解PPI是治疗开发的关键.
  • 目前用于预测结合亲和力的方法通常需要3D结构,从而限制了它们的适用性.

研究的目的:

  • 开发基于序列的计算框架Seq2Bind,用于预测蛋白质与蛋白质的结合亲和力,并识别关键的结合残留物.
  • 评估精细调整的蛋白质语言模型 (PLM) 对此任务的性能.
  • 提供一个网络服务器工具,用于快速选PPI.

主要方法:

  • 在SKEMPI 2.0数据集上微调了四个PLM架构 (ProtBERT,ProtT5,ESM2,双向LSTM).
  • 评估了来自蛋白质数据库的6063个二元蛋白质的模型,使用了氨酸突变发生的数据.
  • 使用N因素指标评估性能,并与结构对接 (HADDOCK3) 和人类蛋白质复合体的基于突变的基线进行比较.

主要成果:

  • ESM2和ProtBERT显示了高的接口残留回收率 (分别为67.4%和68.2%在N-因子=3).
  • 使用ESM2和ProtBERT的Seq2Bind在人类蛋白质复合体上表现优于HADDOCK3 (37.2%和35.1%对比32.1%在N-factor=2).
  • 基于序列的方法成功处理了无序的蛋白质.

结论:

  • Seq2Bind提供了一个强大的,基于序列的替代方案,用于预测PPI和识别绑定残留物.
  • 网络服务器可以快速选,并可以指导诸如盲目对接之类的结构方法.
  • 这种方法对加速药物发现和理解细胞机制具有重大意义.