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相关概念视频

Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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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Ligand Binding Sites02:40

Ligand Binding Sites

12.6K
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...
12.6K
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
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.7K
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...
4.7K
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,...
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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InDeepNet:一个使用InDeep的网络平台,用于预测蛋白质中的功能结合点.

Fabien Mareuil1, Rachel Torchet1, Luis Checa Ruano2

  • 1Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France.

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概括

在InDeepNet中预测了蛋白质结合部位及其适合药物开发的位置. 这个平台帮助研究人员通过评估蛋白质-连接体相互作用和构造变化来识别潜在的药物标.

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科学领域:

  • 计算生物学是一种计算生物学.
  • 结构生物学是结构生物学.
  • 药物发现 药物发现

背景情况:

  • 预测蛋白质结合部位对于理解蛋白质与蛋白质相互作用 (PPI) 和识别药物点至关重要.
  • 现有的计算方法往往难以评估PPI的结合性,特别是考虑到构造变化.

研究的目的:

  • 介绍InDeepNet,一个基于Web的平台,将深度学习集成为绑定站点预测与对联体绑定构造的评估.
  • 为研究人员提供一个可访问的工具来预测结合位点和评估它们对小分子结合的潜力,从而增强基于结构的药物设计.

主要方法:

  • 开发了InDeepNet,该平台结合了InDeep深度学习模型用于绑定位预测和InDeepHolo用于评估连接体绑定 (全体) 构造.
  • 允许用户从各种来源 (内部,PDB,AlphaFold) 上传蛋白质结构进行分析.
  • 集成的Mol*用于预测结合地点的交互式3D可视化.

主要成果:

  • InDeepNet成功地预测了蛋白质和小分子的潜在结合点.
  • 该平台有助于为小分子结合选择最佳形状,这对于药物设计至关重要.
  • InDeepNet提供了一个直观的界面,消除了对专业编码或高性能计算的需求.

结论:

  • InDeepNet简化了PPI目标的评估和可连接性预测.
  • 该平台民主化了对用于药物发现和针对PPI的治疗开发的先进预测建模的访问.