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相关概念视频

Ligand Binding Sites02:40

Ligand Binding Sites

12.8K
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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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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Leaky Scanning02:28

Leaky Scanning

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During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
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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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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
Usually, Upf3 binds to an Exon Junction Complex (EJC) at mRNA splice sites. If a ribosome fully translates the mRNA,...
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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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相关实验视频

Updated: Jun 16, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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SPRank─一种基于知识的评分功能,用于RNA-基体位预测和虚拟查.

Yuanzhe Zhou1, Yangwei Jiang1, Shi-Jie Chen2

  • 1Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211-7010, United States.

Journal of chemical theory and computation
|August 16, 2024
PubMed
概括
此摘要是机器生成的。

SPRank是一个新的计算工具,可以准确地预测RNA-连接体结合模式,并排列结合亲和力. 这一进步有助于通过改进的虚拟查发现新的RNA向药物.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

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相关实验视频

Last Updated: Jun 16, 2025

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16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.6K
RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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科学领域:

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

背景情况:

  • 针对RNA的治疗方法越来越重要,需要准确的RNA-小化合物相互作用计算模型.
  • 现有的评分功能擅长预测绑定模式,但缺乏对虚拟选的彻底验证.
  • 可靠的评分功能对于预测原生结合姿势和排名连接体亲属性至关重要.

研究的目的:

  • 开发和验证SPRank,一种用于RNA - 连接体相互作用的新型评分函数.
  • 解决虚拟选应用程序当前评分功能的局限性.
  • 为了提高预测结合模式和关联性在RNA-合体复杂模型中的准确性.

主要方法:

  • 斯普兰克集成机器学习和基于知识的方法,使用加权的代策略.
  • 该方法采用第三方对接软件 (rDock,AutoDock Vina) 来对抗RNA组合的灵活带采样.
  • 捕获RNA和配体的形态灵活性,以增强相互作用建模.

主要成果:

  • 在四个不同的测试组 (122,42,55,71个复合体) 中,SPRank在现有的评分功能上表现出了卓越的性能.
  • 该工具在虚拟查任务中表现出更高的有效性,特别是在HIV-1 TAR组合中.
  • 严格的测试证实了RNA-配体复杂相互作用的增强预测能力.

结论:

  • 斯普兰克为RNA - 干相互作用的计算建模提供了显著的进步.
  • 它在结合模式预测和虚拟查方面的改进性能使其成为RNA向药物设计的有价值工具.
  • 自由访问的源代码和数据集有助于进一步的药物发现研究和应用.