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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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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...
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Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Conservation of Protein Domains02:26

Conservation of Protein Domains

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3.1K
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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Structural Protein Function01:56

Structural Protein Function

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2.7K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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相关实验视频

Updated: Jul 4, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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根据结构相似性的功能域注释.

Poorya Mirzavand Borujeni1, Reza Salavati1,2

  • 1Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada.

NAR genomics and bioinformatics
|February 1, 2024
PubMed
概括
此摘要是机器生成的。

结构相似性提供了一种强大的新方法来注释蛋白质域,优于传统的基于序列的方法. 这种方法成功地识别了Trypanosoma brucei中的400多个新域,增强了功能注释能力.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
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相关实验视频

Last Updated: Jul 4, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
12:04

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

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科学领域:

  • 结构生物学是结构生物学.
  • 生物信息学是一种生物信息学.
  • 蛋白质域注释 蛋白质域注释

背景情况:

  • 传统的 *in silico* 功能注释依赖于序列相似性 (例如,Pfam).
  • 结构性保存可以超过序列保存,为改进的注释提供了潜力.
  • 像AlphaFold2这样的进步增加了高质量的蛋白质结构的可用性,使基于结构的方法成为可能.

研究的目的:

  • 评估使用结构相似性的Pfam域注释的可行性.
  • 开发和测试一种利用结构数据进行蛋白质域注释的新方法.
  • 为了增强 *Trypanosoma brucei* 蛋白质组的功能注释.

主要方法:

  • 创建了代表Pfam种子的细分蛋白质结构的数据库.
  • 使用Foldseek对*Trypanosoma brucei*结构体与数据库进行超快的结构调整.
  • 基于顶部非重叠的结构对齐结果的注释域.

主要成果:

  • 在T. brucei*蛋白质组中发现了400多个新的Pfam域.
  • 基于结构的注释超过了基于序列的工具 (Pfam,Pfam-N) 的性能.
  • 一些新的领域预测被手动验证,证实了该方法的准确性.

结论:

  • 基于蛋白质结构的域注释是一个可行的和强大的策略.
  • 这种方法显著提高了新型蛋白质域的发现,特别是在进化上遥远的生物体中.
  • 未来的工作可以进一步完善基于结构的注释技术,用于更广泛的应用.