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相关概念视频

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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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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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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相关实验视频

Updated: Jul 9, 2025

Estimation of Contact Regions Between Hands and Objects During Human Multi-Digit Grasping
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开放式ComBind:利用未标记的数据进行改进的绑定姿势预测.

Andrew T McNutt1, David Ryan Koes2

  • 1Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.

Journal of computer-aided molecular design
|December 7, 2023
PubMed
概括
此摘要是机器生成的。

Open-ComBind通过使用多个连接体的数据来增强分子对接,以改善蛋白质-连接体姿势预测. 这种开源工具提高了选精度高达5%,并将平均连接体RMSD降低了9%.

关键词:
机器学习是机器学习.分子对接是分子对接.这是开源的,开源的.基于结构的药物设计.

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科学领域:

  • 计算化学计算化学
  • 药物发现 药物发现 药物发现
  • 结构生物学 结构生物学

背景情况:

  • 准确预测连接体结合的姿势对于in silico药物发现至关重要.
  • 传统的分子对接通常分析单个连接体,忽视了同一受体的多个连接体之间的共享结合相互作用.
  • 现有的方法缺乏有效的方式来利用来自多个配体的信息来完善姿势选择.

研究的目的:

  • 为了介绍Open-ComBind,一个开源的分子对接管道.
  • 通过整合来自多个联体的信息来增强联体姿势选择.
  • 为了提高预测非共价蛋白-连接体结合相互作用的准确性.

主要方法:

  • 开发了Open-ComBind,这是ComBind管道的可访问版本.
  • 创建了连接体姿势对之间的特征相似性的分布.
  • 将近本地姿势与所有样本对接姿势进行比较,以捕捉特征的可能性.
  • 结合相似性分布与每个连接体对接分数用于姿势选择.

主要成果:

  • 提高了总体姿势选择5%的高亲和度联体和4.5%的同源系列.
  • 在基准数据集中将连接体的平均根平均平方偏差 (RMSD) 降低了9.0%.
  • 通过利用多连接体数据,证明了更好的姿势预测性能.

结论:

  • Open-ComBind有效地提高了分子对接中的联结体姿势预测准确性.
  • 该开源工具为in silico药物发现管道提供了宝贵的增强.
  • 利用多连接体信息在预测蛋白质-连接体结合位置方面具有显著的优势.