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Related Concept Videos

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...
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,...

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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

InterPro protein classification.

Jennifer McDowall1, Sarah Hunter

  • 1EMBL Outstation, European Bioinformatics Institute (EBI), Cambridge, UK.

Methods in Molecular Biology (Clifton, N.J.)
|November 18, 2010
PubMed
Summary
This summary is machine-generated.

The InterPro database integrates protein signatures from 11 sources to automatically annotate protein sequences. This resource aids in classifying vast amounts of data generated by rapid sequencing technologies.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput sequencing generates vast numbers of protein sequences, overwhelming manual annotation capabilities.
  • A growing proportion of newly sequenced proteins remain unannotated, creating a data bias.
  • Automatic annotation tools are crucial for keeping pace with sequence generation and ensuring data utility.

Purpose of the Study:

  • To review the signature methods integrated within the InterPro database.
  • To provide an overview of the InterPro resource as a powerful protein annotation tool.
  • To highlight InterPro's scalability for analyzing entire genomes.

Main Methods:

  • Integration of protein signatures from 11 distinct databases (e.g., Pfam, PROSITE, SMART) into a unified resource.
  • Development of protein signatures using methods ranging from conserved motifs to Hidden Markov Models (HMMs).
  • Provision of a downloadable version, InterProScan, for local pipeline integration and large-scale genome analysis.

Main Results:

  • The InterPro database consolidates diverse protein signature approaches for comprehensive annotation.
  • InterProScan enables scalable, automated protein annotation, addressing the challenge of unannotated sequences.
  • InterPro links protein signatures with structural information (PDB, CATH, SCOP) and homology models (ModBase, SwissModel) for integrated analysis.

Conclusions:

  • InterPro serves as a vital, open-source resource for automated protein annotation and classification.
  • The database effectively mitigates the bias towards unannotated sequences resulting from rapid sequencing.
  • InterPro's integration of signature methods and structural data enhances its value for biological research.