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Related Concept Videos

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-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 Networks02:26

Protein Networks

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,...
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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

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Updated: Jun 29, 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

Automatically extracting functionally equivalent proteins from SwissProt.

Lisa E M McMillan1, Andrew C R Martin

  • 1Research Department of Structural & Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK. mcmillan@biochem.ucl.ac.uk

BMC Bioinformatics
|October 8, 2008
PubMed
Summary
This summary is machine-generated.

We developed FOSTA, a tool to automatically identify functionally equivalent proteins (FEPs) across species using UniProtKB/Swiss-Prot annotations. This resource aids large-scale analysis by extracting FEP groups, overcoming limitations of orthology and manual extraction.

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Area of Science:

  • Bioinformatics
  • Proteomics
  • Computational Biology

Background:

  • Identifying functionally equivalent proteins (FEPs) across species is crucial but challenging, as orthology doesn't always guarantee functional equivalence.
  • Manual extraction of FEPs from databases like UniProtKB/Swiss-Prot is time-consuming and not scalable.
  • Existing resources lack automated methods for large-scale FEP group extraction.

Purpose of the Study:

  • To develop an automated database, FOSTA, for extracting groups of functionally equivalent proteins (FEPs).
  • To leverage UniProtKB/Swiss-Prot functional annotations for reliable FEP identification.
  • To facilitate large-scale biological analyses requiring functionally conserved proteins.

Main Methods:

  • Developed FOSTA, an automated system for generating a database of FEPs.
  • Employed a text mining approach to analyze functional annotations in UniProtKB/Swiss-Prot.
  • Filtered candidate homologous proteins to remove functionally diverged instances based on annotation data.

Main Results:

  • FOSTA successfully extracts groups of proteins annotated as functionally equivalent in UniProtKB/Swiss-Prot.
  • Manual analysis of five protein families confirmed high performance of the FEP extraction method.
  • Comparison with manually verified datasets demonstrated very good performance, validating FOSTA's accuracy.

Conclusions:

  • FOSTA provides an automated solution for extracting FEP groups, enhancing large-scale biological research.
  • The study confirms the high quality of UniProtKB/Swiss-Prot functional annotations and FOSTA's ability to interpret them.
  • FOSTA can identify annotation inconsistencies and suggests improvements for UniProtKB/Swiss-Prot to aid future text-mining efforts.