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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...
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...
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...
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...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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Related Experiment Video

Updated: May 13, 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

Protein function prediction using domain families.

Robert Rentzsch1, Christine A Orengo

  • 1Robert Koch Institut, Research Group Bioinformatics Ng4, Nordufer 20, 13353 Berlin, Germany. rentzschr@rki.de

BMC Bioinformatics
|March 22, 2013
PubMed
Summary
This summary is machine-generated.

Researchers developed functional families (FunFams) to predict protein functions. This domain-based approach outperformed sequence comparisons in the CAFA 2011 experiment, showing improved protein function prediction accuracy.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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Last Updated: May 13, 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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Protein Function Prediction

Background:

  • Predicting protein function is crucial in biology.
  • Existing methods often struggle with accuracy and scalability.
  • Domain-based approaches offer a promising avenue for functional annotation.

Purpose of the Study:

  • To assess the utility of 'functional families' (FunFams) for predicting whole protein functions.
  • To develop and validate a novel protocol for generating FunFams.
  • To compare the performance of FunFams against traditional sequence clustering methods.

Main Methods:

  • Developed a protocol combining sequence clustering and supervised evaluation using Gene Ontology (GO) annotations.
  • Grouped domain sequences into families based on GO annotations of parent proteins.
  • Applied FunFams probabilistically with GO terms for the CAFA 2011 experiment, including multi-domain protein integration.

Main Results:

  • FunFams demonstrated superior resemblance to enzyme (domain) families compared to sequence clustering alone.
  • The domain-based FunFam approach ranked among the top ten methods in the CAFA 2011 experiment.
  • Outperformed simple pairwise whole-protein sequence comparisons in function prediction.

Conclusions:

  • Functional families (FunFams) provide a robust framework for accurate protein function prediction.
  • The developed protocol effectively leverages domain information and GO annotations.
  • This domain-centric strategy represents a significant advancement in computational protein function annotation.