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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
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

5.6K
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...
5.6K
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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相关实验视频

Updated: May 22, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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ProtCB-bind:使用一组分类器预测蛋白质-碳水化合物结合部位.

Divnesh Prasad1, Ronesh Sharma2, M G M Khan1

  • 1School of Information Technology, Engineering, Mathematics and Physics, The University of the South Pacific, Suva, Fiji.

Carbohydrate research
|March 14, 2025
PubMed
概括

这项研究引入了ProtCB-Bind,一种新的计算模型,可以准确预测蛋白质与碳水化合物的相互作用. 该工具增强了对生物功能必不可少的生物分子结合事件的理解.

关键词:
分类器组合组合是一个分类器组合.基于概率的预测.蛋白质碳水化合物-蛋白质碳水化合物基于序列的技术 基于序列的技术

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科学领域:

  • 生物化学 生物化学
  • 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:

  • 蛋白质和碳水化合物是许多生物过程中必不可少的基本生物分子,包括免疫反应和能量储存.
  • 识别蛋白质-碳水化合物结合区域对于理解这些重要相互作用至关重要.
  • 目前的计算方法需要改进,以准确预测这些相互作用.

研究的目的:

  • 开发和验证ProtCB-Bind,这是一个用于预测蛋白质-碳水化合物相互作用的新型计算模型.
  • 利用先进的机器学习和自然语言处理 (NLP) 技术来提高预测准确度.
  • 为研究蛋白质与碳水化合物结合的研究人员提供可访问的工具.

主要方法:

  • ProtCB-Bind采用了一组机器学习分类器,用于预测,采用一种共同的平均方法.
  • 该模型使用基于序列的,基于进化的蛋白质特征和氨基酸物理化学性质进行训练.
  • 集成了基于变压器的NLP功能,以提高预测性能.

主要成果:

  • ProtCB-Bind系统地针对分类器和特征组合进行了优化.
  • 该模型在与SPRINT-CBH,StackCB-Pred和StackCB-Embed等现有最先进的预测器相比显示出更高的性能.
  • 在基准数据集上,总体绩效大约有3%的改善.

结论:

  • ProtCB-Bind在蛋白质与碳水化合物相互作用的计算预测方面取得了重大进展.
  • 该模型的增强精度和NLP特征的整合为生物分子识别提供了有价值的见解.
  • 源代码是公开的,这有助于在该领域进行进一步的研究和应用.