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相关概念视频

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.7K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.7K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Conservation of Protein Domains02:26

Conservation of Protein Domains

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3.1K
Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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...
4.1K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.7K
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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Updated: May 24, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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学习最大限度地跨越表示方式 改善蛋白质功能注释

Jiaqi Luo1, Yunan Luo1

  • 1School of Computational Science and Engineering, Georgia Institute of Technology.

bioRxiv : the preprint server for biology
|March 3, 2025
PubMed
概括
此摘要是机器生成的。

新的深度学习框架MSRep通过解决数据不平衡来改善蛋白质功能注释. 它提高了对常见和罕见蛋白质功能的预测准确度,有助于研究未表征的蛋白质.

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科学领域:

  • 计算生物学是一种计算生物学.
  • 生物信息学是一种生物信息学.
  • 机器学习 机器学习

背景情况:

  • 自动化蛋白质功能注释对于理解生物过程,医学和生物技术至关重要.
  • 现有的方法与不平衡的数据作斗争,导致对未经研究的蛋白质功能的表现不佳.
  • 这种不平衡源于数据收集和蛋白质进化的偏见.

研究的目的:

  • 开发MSRep,一个新的深度学习框架,以解决蛋白质功能注释中的数据不平衡问题.
  • 为了提高对表现良好和表现不足的蛋白质功能的预测准确度.
  • 为了提高蛋白质功能预测模型的概括性.

主要方法:

  • MSRep使用一种由神经崩 (NC) 启发的新型损失函数来改进预训练的蛋白质语言模型.
  • 该框架诱导了一个类似NC的结构,以确保嵌入空间中所有函数类的平衡表示.
  • 通过四个不同的蛋白质功能注释任务 (EC 号码,Gene3D,Pfam,GO 术语) 进行评估.

主要成果:

  • 在所有测试的注释任务中,MSRep表现出卓越的预测性能.
  • 该框架显著提高了对已研究完善和未研究完善的蛋白质功能的准确性.
  • MSRep的性能优于现有的几种最先进的蛋白质注释工具.

结论:

  • MSRep有效地解决了蛋白质功能注释中数据不平衡的挑战.
  • 该方法增强了研究不足的功能和未表征的蛋白质的注释.
  • MSRep对推进蛋白质功能研究和加速生物发现具有前途.