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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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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.

Keywords:

functional family protein classification protein domain protein structure superfamily

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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.