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09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
16.2K
Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.
Ian Sillitoe1, Tony Lewis1, Christine Orengo1
1University College London, London, United Kingdom.
Current Protocols in Bioinformatics
|June 20, 2015
Summary
The CATH-Gene3D resource classifies protein structures and identifies evolutionary relatives. It integrates structural data with sequence profiles and functional annotations for comprehensive protein analysis.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein evolution
Background:
- The CATH database classifies protein structures from the Protein Data Bank (PDB).
- Structural domains are grouped into superfamilies based on evolutionary divergence.
- Gene3D extends CATH by scanning sequence profiles to find related proteins.
Purpose of the Study:
- To describe the combined CATH-Gene3D resource for protein structure and evolution analysis.
- To detail how to access and interpret information from CATH-Gene3D.
- To highlight the integration of diverse biological annotations.
Main Methods:
- Classification of protein structures into domains and superfamilies.
- Sequence profile scanning using Gene3D against large protein databases.
- Integration of external database annotations (e.g., enzyme active sites, GO functions, mutations).
Main Results:
- The CATH-Gene3D resource provides confident predictions of protein structural folds, domain organization, and evolutionary relationships.
- It offers integrated annotations from multiple external biological databases.
- Web pages, downloadable files, and web services are available for data access.
Conclusions:
- The CATH-Gene3D resource is a valuable tool for understanding protein structure, function, and evolution.
- It facilitates comprehensive analysis by combining structural classification with sequence and functional data.
- Users can access and utilize this information through various platforms.
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