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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 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...
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 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...
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...
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,...

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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

CombFunc: predicting protein function using heterogeneous data sources.

Mark N Wass1, Geraint Barton, Michael J E Sternberg

  • 1Centre for Bioinformatics, Imperial College London, London, SW7 2AZ, UK. mark.wass04@imperial.ac.uk

Nucleic Acids Research
|May 30, 2012
PubMed
Summary
This summary is machine-generated.

Predicting protein function is crucial for understanding uncharacterized proteins. The CombFunc web server integrates multiple data types for accurate Gene Ontology (GO) based function predictions, improving annotation efforts.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • A small fraction of known proteins are functionally characterized.
  • Protein function prediction is vital for annotating uncharacterized proteins.
  • Various data sources, including sequence, structure, and gene expression, are used for prediction.

Purpose of the Study:

  • To present the CombFunc web server for Gene Ontology (GO)-based protein function predictions.
  • To integrate existing and novel function prediction approaches into a single platform.
  • To provide a tool for proposing annotations for uncharacterized proteins.

Main Methods:

  • CombFunc integrates ConFunc with methods utilizing protein sequence, gene expression, and protein-protein interaction data.
  • Benchmarking was performed on a dataset of 1686 proteins.
  • Predictions are based on Gene Ontology (GO) terms.

Main Results:

  • CombFunc achieved 0.71 precision and 0.64 recall for molecular function GO terms.
  • For biological process GO terms, CombFunc obtained 0.74 precision and 0.41 recall.
  • The CombFunc web server is publicly available.

Conclusions:

  • CombFunc offers a robust approach for protein function prediction by integrating diverse biological data.
  • The web server facilitates improved functional annotation of proteins.
  • Accurate function prediction is essential for advancing biological research.