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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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对生物医学实体链接模型的全面评估

David Kartchner1,2, Jennifer Deng2, Shubham Lohiya2

  • 1Enveda Biosciences.

Proceedings of the Conference on Empirical Methods in Natural Language Processing. Conference on Empirical Methods in Natural Language Processing
|May 17, 2024
PubMed
概括
此摘要是机器生成的。

这项研究评估了九个生物医学实体链接 (BioEL) 模型,发现当前的方法与基因/蛋白质链接和上下文集成存在困难. 一个统一的框架和模型被释放,以帮助未来的研究.

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科学领域:

  • 生物医学信息学 生物医学信息学
  • 自然语言处理自然语言处理.
  • 计算生物学 计算生物学

背景情况:

  • 生物医学实体链接 (BioEL) 对于将文本提及与UMLS和MeSH等结构化知识库连接至关重要.
  • 现有的生物EL模型有很大的差异,需要采用标准化的评估方法.

研究的目的:

  • 通过使用统一的框架,全面评估九个最先进的生物EL模型.
  • 确定当前BioEL方法在准确性,速度,可用性,概括性和适应性方面的优缺点.
  • 为未来的研究提供可重复的评估框架和发布的模型.

主要方法:

  • 开发并应用一个统一的框架来评估九个BioEL模型.
  • 基于准确性,速度,易用性,概括性和适应新本体学/数据集的可比模型.
  • 量化了预处理步骤的影响,包括缩写检测.

主要成果:

  • 目前的BioEL模型表现出显著的性能差距,特别是在将基因和蛋白质联系起来.
  • 模型通常很难有效地结合上下文信息,以获得准确的实体歧义.
  • 在不同的评估标准和数据集中观察到性能变化.

结论:

  • 对于改进的BioEL方法存在重大需求,特别是对于基因和蛋白质实体.
  • 加强上下文利用对于提高生物EL准确性至关重要.
  • 发布的统一框架和模型将成为BioEL研究社区的宝贵资源.