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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...
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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Updated: Jun 19, 2026

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

PROSITE, a protein domain database for functional characterization and annotation.

Christian J A Sigrist1, Lorenzo Cerutti, Edouard de Castro

  • 1Structural Biology and Bioinformatics Department, University of Geneva, Swiss Institute of Bioinformatics, Centre Médical Universitaire, CH-1211 Geneva 4, Switzerland. christian.sigrist@isb-sib.ch

Nucleic Acids Research
|October 28, 2009
PubMed
Summary

The PROSITE database enhances protein annotation using patterns and profiles, with ProRule rules improving accuracy. Recent developments include a new profile building method and improved data integration for better functional characterization.

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Last Updated: Jun 19, 2026

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Published on: November 3, 2011

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Published on: October 3, 2018

Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Proteomics

Background:

  • PROSITE database provides documentation for protein domains, families, and functional sites.
  • ProRule rules enhance PROSITE profiles and patterns by incorporating critical amino acid information.
  • PROSITE is crucial for annotating UniProtKB/Swiss-Prot entries, with ~70% of specific domains annotated.

Purpose of the Study:

  • To improve the functional characterization of protein domains.
  • To introduce advancements in PROSITE's profile building and data integration methods.
  • To enhance the discriminatory power of protein domain identification tools.

Main Methods:

  • Utilized an annotated multiple sequence alignment format (AMSA) for generalized profiles.
  • Migrated ScanProsite to a high-performance computing cluster (Vital-IT).
  • Adopted the Distributed Annotation System (DAS) for seamless data integration.

Main Results:

  • PROSITE release 20.54 includes 1308 patterns, 863 profiles, and 869 ProRules.
  • Approximately 70% of relevant Swiss-Prot domains were annotated using PROSITE descriptors.
  • New methods focus on subfamily-specific profiles and weighting functionally important residues.

Conclusions:

  • PROSITE developments aim for more precise functional characterization of protein domains.
  • Enhanced data integration and computational resources improve PROSITE's utility.
  • The database continues to be a vital resource for protein annotation and analysis.