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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 form...

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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

Protein subfamily assignment using the Conserved Domain Database.

Jessica H Fong1, Aron Marchler-Bauer

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA. fongj@ncbi.nlm.nih.gov

BMC Research Notes
|November 19, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for protein domain assignment, improving accuracy by considering domain hierarchies. The developed heuristics significantly reduce classification errors in protein domain annotation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein domains are conserved units used for sequence classification and function inference.
  • Overlapping domain models often require methods to select the correct domain annotation.
  • The Curated Domain Database (CDD) provides NCBI-curated domain models.

Purpose of the Study:

  • To develop a method for assigning NCBI-curated domains from the CDD.
  • To account for the hierarchical organization of homologous domain models.
  • To improve the accuracy of protein domain annotation.

Main Methods:

  • Analysis of alignment scores for NCBI-curated domain assignments.
  • Development of heuristics based on score sorting and domain-specific thresholds.
  • Incorporation of a domain subfamily assignment rule.

Main Results:

  • Identifying correct models among closely related ones is challenging.
  • Heuristics effectively reduce classification error.
  • The proposed method corrects nearly 90% of misclassifications due to missing subfamilies, replacing them with more general assignments.

Conclusions:

  • The domain subfamily assignment rule has been integrated into CD-Search software.
  • The method significantly enhances pre-calculated domain annotations in NCBI's Entrez resource.