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

Proteomics01:33

Proteomics

7.1K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.1K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
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

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

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

MolViewStories: Interactive molecular storytelling.

Protein science : a publication of the Protein Society·2026
Same author

Structure-activity relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures.

Chemical science·2026
Same author

RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.

Nucleic acids research·2025
Same author

From sequence to protein structure and conformational dynamics with artificial intelligence/machine learning.

Structural dynamics (Melville, N.Y.)·2025
Same author

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations.

Nucleic acids research·2025

相关实验视频

Updated: May 22, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.1K

多个尺度的结构相似性嵌入搜索在整个蛋白质组.

Joan Segura1, Ruben Sanchez-Garcia2, Sebastian Bittrich1

  • 1Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA.

bioRxiv : the preprint server for biology
|March 17, 2025
PubMed
概括

一种新的人工智能驱动的方法使得快速可扩展的3D生物分子结构相似性搜索成为可能. 这种方法有效地比较了庞大的结构数据集,克服了大规模检索传统对齐方法的局限性.

更多相关视频

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

68.4K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K

相关实验视频

Last Updated: May 22, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

3.1K
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

68.4K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.3K

科学领域:

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

背景情况:

  • 由人工智能/深度学习 (DL) 预测推动的3D生物分子结构的指数增长,需要有效的搜索工具.
  • 传统的结构比较方法 (例如,结构叠加) 是计算密集的,并且在大型数据集中不太适应.

研究的目的:

  • 开发一个可扩展和有效的战略,用于搜索3D生物分子结构相似性.
  • 为了使广泛的存储库能够导航,其中包含实验确定结构和AI/DL预测模型.

主要方法:

  • 利用蛋白质语言模型和深度神经网络将3D结构转换为固定长度向量.
  • 实现了矢量数据库,以进行高效的大规模结构检索和比较.
  • 训练模型来预测单域结构的TM分数.

主要成果:

  • 开发的方法证明了搜索庞大的结构存储库的可扩展性.
  • 该模型准确地识别了全长蛋白质和多重体组件的3D相似性,并将其推广到单个域之外.
  • 通过向量数据库集成,可以实现高效的大规模结构检索.

结论:

  • 拟议的战略有效地解决了搜索大量3D生物结构数据的挑战.
  • 这种方法为生物分子结构相似性搜索的传统方法提供了一个计算效率高的替代方案.
  • 该方法可方便从各种来源探索和检索结构信息,包括AI/DL预测模型.