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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

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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...
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Ligand Binding Sites02:40

Ligand Binding Sites

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Conserved Binding Sites01:49

Conserved Binding Sites

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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 and Linkage00:49

Ligand Binding and Linkage

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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...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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EvoZymePro-Cat:一种蛋白质 - 配体 - 感知深度学习框架,用于预测酶功能的突变效应.

Ran Xu1, Xinkang Li1, Jianan Sui1

  • 1Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China.

ACS synthetic biology
|December 21, 2025
PubMed
概括

EvoZymePro-Cat (EZPro-Cat) 是一个深度学习平台,用于选酶突变物. 它准确地预测了相对的酶活性,改善了酶的发现和定向进化.

关键词:
在 BANLayer 中,您可以使用酵素酶是一种酶.核聚变的表示形式蛋白质工程工程 蛋白质工程

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科学领域:

  • 生物催化和酶工程 生物催化和酶工程
  • 计算生物学和生物信息学
  • 机器学习在化学中的应用

背景情况:

  • 酶设计是复杂的,因为它拥有庞大的序列空间和相互依赖.
  • 预测酶突变活性是传统方法的挑战.
  • 精确的酶突变查对于生物催化剂至关重要.

研究的目的:

  • 开发一个深度学习平台,EvoZymePro-Cat (EZPro-Cat),用于高效的酶突变查.
  • 通过对对比框架克服绝对活动预测的局限性.
  • 通过改进功能概况来增强酶发现和定向进化.

主要方法:

  • 开发了EvoZymePro-Cat (EZPro-Cat),这是一个集序列,结构和连接物数据的深度学习平台.
  • 利用一对对比框架来预测相对突变活动优势.
  • 使用ESM1b进行蛋白序列编码,并使用Molt5/MACCS进行连接体表示.
  • 集成的结构特征和进化特征与蛋白质 - 配体相互作用的双线性注意力机制.

主要成果:

  • 双对比框架在识别改进的酶突变物方面表现出卓越的表现.
  • 在深度突变扫描数据集上使用几次射击学习策略实现了高预测精度 (AUC 0.908).
  • 该模型有效地捕捉了催化过程中的远程分子间相互作用.
  • 在预测酶动力学 (Km, kcat) 突变效应方面表现出卓越的表现.

结论:

  • EvoZymePro-Cat (EZPro-Cat) 为酶功能分析提供了一种机械和实用的解决方案.
  • 该平台有助于高效的酶发现和定向进化.
  • 双对比方法克服了绝对活动预测中的系统错误.
  • 集成的多模式表示增强了对蛋白内变异函数的理解.