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相关概念视频

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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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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相关实验视频

Updated: Jun 12, 2025

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在40个小分子数据库中的陶托马体冲突.

Devendra K Dhaked1, Marc C Nicklaus1

  • 1Computer-Aided Drug Design Group, Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland 21702, United States.

Journal of chemical information and modeling
|September 24, 2024
PubMed
概括

在所有分析的化学数据库中,都发现了不同分子结构被错误地识别为相同的tautomeric冲突. 这些冲突影响了2.10亿多个结构,突出了提高化学数据标准化的必要性.

科学领域:

  • 化学 化学 化学
  • 化学信息学 化学信息学
  • 计算化学计算化学

背景情况:

  • 化学数据库包含大量的分子结构.
  • 对分子结构的准确表示对于化学研究和药物发现至关重要.
  • 陶托马力学,即在质子和相邻单双键的位置上存在不同分子的存在,可以导致结构模两可.

研究的目的:

  • 在多种化学数据库中识别和量化分体冲突.
  • 评估大规模化学数据中 tautomeric 错误的流行程度和影响.
  • 为了评估现有的分体转换规则的有效性.

主要方法:

  • 分析了40个化学数据库 (总共超过2.10亿个结构).
  • 应用119个分体变换规则 (SMIRKS格式) 来检测冲突.
  • tautomerism 的分类为原型,环链和价值类型.

主要成果:

  • 所有分析的数据库都表现出数据库内部的相互冲突.
  • 在119个测试的分体规则中,79个发现了至少一个冲突.
  • 冲突率通常在百分之十分之一以下,在最大的数据库中翻译为超过10万个案例.

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结论:

  • 陶托马体冲突是化学数据库中普遍存在的问题.
  • 这些发现强调了对强大的算法和对 tautomer 识别的标准化规则的必要性.
  • 改进的数据处理对于可靠的化学信息检索和分析至关重要.