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

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

1.8K
1.8K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.4K
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...
12.4K
Protein Networks02:26

Protein Networks

3.9K
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,...
3.9K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.6K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.6K
Protein Complex Assembly02:41

Protein Complex Assembly

10.5K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.5K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.0K
3.0K

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

Author Correction: Remote loop evolution reveals a complex biological function for chitinase enzymes beyond the active site.

Nature communications·2026
Same author

The role of the tryptophan-rich allosteric network and sodium egress in GPCR activation.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Molecular Design with Artificial Intelligence: Progress and Perspectives for Small Molecules.

Chemical reviews·2026
Same author

DiffBreed: automatic differentiation enables efficient gradient-based optimization of breeding strategies.

Bioinformatics (Oxford, England)·2025
Same author

Harnessing Explainable AI to Explore Structure-Activity Relationships in Artificial Olfaction.

ACS applied materials & interfaces·2025
Same author

GPepT: A Foundation Language Model for Peptidomimetics Incorporating Noncanonical Amino Acids.

ACS medicinal chemistry letters·2025

相关实验视频

Updated: May 16, 2025

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

18.3K

HDXRank:一种深度学习框架,用于使用-交换数据对蛋白质复杂预测进行排名.

Liyao Wang1,2, Andrejs Tučs1,2, Songting Ding1

  • 1Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8561, Japan.

Journal of chemical theory and computation
|May 14, 2025
PubMed
概括

HDXRank是一个新的图形神经网络 (GNN) 工具,它使用-交换 (HDX) 数据来准确排名蛋白质复杂模型. 这种方法改善了分子识别和生物机制的预测.

更多相关视频

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes
11:32

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

7.9K
Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
09:18

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Published on: April 17, 2017

9.8K

相关实验视频

Last Updated: May 16, 2025

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry
11:37

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Published on: November 29, 2013

18.3K
A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes
11:32

A Hydrogen-Deuterium Exchange Mass Spectrometry HDX-MS Platform for Investigating Peptide Biosynthetic Enzymes

Published on: May 4, 2020

7.9K
Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics
09:18

Time-resolved ElectroSpray Ionization Hydrogen-deuterium Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

Published on: April 17, 2017

9.8K

科学领域:

  • 结构生物学是结构生物学.
  • 计算生物学是一种计算生物学.
  • 生物物理学的生物物理.

背景情况:

  • 准确的蛋白质-蛋白质复杂结构建模对于理解生物过程至关重要.
  • -交换 (HDX) 实验提供了对蛋白质结合接口的见解.
  • 将HDX数据集成到建模中可以提高预测准确性.

研究的目的:

  • 开发HDXRank,一个基于图形神经网络 (GNN) 的框架,用于使用HDX数据对蛋白质复杂结构进行排名.
  • 评估HDXRank提高蛋白质复杂模型准确性的能力.

主要方法:

  • 开发了HDXRank,这是一个基于HDX数据对齐的GNN框架,用于基于HDX数据对齐的候选结构排名.
  • 在精心策划的HDX数据集上训练HDXRank以捕捉本地结构特征.
  • 集成HDXRank与现有的建模工具 (刚性对接,AlphaFold).

主要成果:

  • HDXRank通过与HDX实验数据对齐,有效地对蛋白质复杂模型进行排名.
  • 该框架成功地优先考虑了功能相关的模型.
  • HDXRank 提高了各种蛋白质标的预测质量.

结论:

  • HDXRank提供了一种多功能方法,通过结合HDX数据来增强蛋白质复合体建模.
  • 这一框架将HDX配置对齐转化为一种有价值的模型质量指标.
  • HDXRank显示了促进分子识别研究的巨大潜力.