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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...
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,...
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,...
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-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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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

Homology-based inference sets the bar high for protein function prediction.

Tobias Hamp1, Rebecca Kassner, Stefan Seemayer

  • 1TUM, Department of Informatics, Bioinformatics & Computational Biology - I12 Boltzmannstr, 3, 85748 Garching/Munich, Germany.

BMC Bioinformatics
|March 22, 2013
PubMed
Summary

Predicting protein function using homology is challenging. This study introduces new homology-based methods that set a benchmark for future protein function prediction advancements.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Protein Science

Background:

  • Predicting protein function is crucial for understanding biological systems.
  • De novo prediction methods should surpass random guessing and homology-based inference.
  • Establishing a robust baseline for protein function prediction is essential for evaluating new algorithms.

Purpose of the Study:

  • To develop and evaluate homology-based methods for protein function prediction.
  • To establish a performance benchmark for protein function prediction.
  • To propose a novel metric for assessing the accuracy of protein function predictions.

Main Methods:

  • Development of several protein function prediction methods relying exclusively on homology.
  • Implementation of these methods within the context of the Critical Assessment of Function Annotations (CAFA) challenge.
  • Introduction of a new quantitative measure for comparing predicted and experimental protein annotations.

Main Results:

  • The most successful baseline homology-based method achieved a high ranking in CAFA1.
  • The best combination of homology-based methods performed comparably to top-tier prediction methods.
  • Significant variation in performance among different homology-based methods was observed, with unexpected reasons for differences.

Conclusions:

  • Homology-based inference, while conceptually simple, requires careful implementation for optimal performance.
  • The developed methods provide a strong baseline for future protein function prediction research.
  • A new annotation comparison measure was proposed to better reflect functional details and user expectations.