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相关概念视频

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...
4.4K
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...
13.2K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.9K
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...
4.9K
Protein Families02:47

Protein Families

15.8K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
15.8K
Protein Networks02:26

Protein Networks

4.1K
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,...
4.1K

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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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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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使用PoSSuM数据库探索蛋白质上的结合点,用于功能预测.

Kentaro Tomii1, Kazuyoshi Ikeda2,3

  • 1Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan. k-tomii@aist.go.jp.

Methods in molecular biology (Clifton, N.J.)
|July 29, 2025
PubMed
概括
此摘要是机器生成的。

PoSSuM数据库及其扩展 (PoSSuMds,PoSSuMAg,PoSSuMAF) 提供了有价值的工具,用于预测蛋白质功能,并通过使用3D结构分析蛋白质-连接体结合点的相似性来帮助药物发现.

关键词:
阿尔法折叠是什么意思阿尔法折叠抗体抗原相互作用绑定网站 绑定网站数据库数据库数据库是一个数据库.药物发现 药物发现有关联体的连接体这就是PoSSuM的意义.蛋白配体相互作用寻找相似性的搜索

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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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An Integrated Approach for Microprotein Identification and Sequence Analysis
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相关实验视频

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

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科学领域:

  • 结构生物信息学 结构生物信息学
  • 计算生物学是一种计算生物学.
  • 药物发现 药物发现

背景情况:

  • 蛋白质的功能与其与其他分子的相互作用密切相关.
  • 分析蛋白质连接体复杂结构有助于预测生物功能和推动药物发现.
  • 现有的数据库提供了有关蛋白质-连接体相互作用的宝贵数据.

研究的目的:

  • 介绍并展示PoSSuM数据库及其相关资源的实用性.
  • 为了促进生物功能的预测,并支持药物发现和开发工作.
  • 展示这些数据库用于分析蛋白质结合位点的应用.

主要方法:

  • 构建和发布PoSSuM数据库,根据3D结构编译基于蛋白质结合点的相似性搜索结果.
  • 开发PoSSuMds用于药物结合部位相似性搜索.
  • 扩展到PoSSuMAg用于抗体-抗原结合点的相似性和PoSSuMAF用于AlphaFold预测的人类蛋白质结构中的结合点.

主要成果:

  • PoSSuM数据库提供已知和假定的蛋白质结合位点的编译相似性搜索结果.
  • PoSSuMds,PoSSuMAg和PoSSuMAF将这些功能扩展到药物结合部位,抗体-抗原相互作用和预测蛋白质结构.
  • 这些数据库可以在各种蛋白质类型和环境中高效地搜索类似的结合点.

结论:

  • PoSSuM数据库套件为结构生物信息学和药物发现提供了强大的资源.
  • 利用这些数据库可以显著提高蛋白质功能的预测和候选药物的识别.
  • 展示的例子说明了利用这些计算工具的实际应用.