Extending CATH: increasing coverage of the protein structure universe and linking structure with function

Area of Science:

• Structural biology
• Bioinformatics
• Protein classification

Background:

• The CATH database classifies protein structures into classes, architectures, topologies, and homologies.
• Previous versions focused on structural genomics and transmembrane proteins, increasing fold space coverage.
• Version 3.3 contained 128,688 domains and 2386 superfamilies.

Purpose of the Study:

• To enhance the presentation of sequence and functional information for CATH superfamilies.
• To improve the search functionality and user experience of the CATH database.
• To increase the representation of novel protein structures within the CATH database.

Main Methods:

• Implemented improved presentation of sequence and functional data for CATH superfamilies.
• Integrated structural alignments of related proteins with functional annotations and conserved residue details.
• Deployed the Solr search server for a more efficient CATH search function.
• Utilized the Catalyst web framework for building the CATH v3.4 webpages.

Main Results:

• CATH version 3.4 significantly improved the display of functional and sequence data for superfamilies.
• Superfamily pages now showcase functional and structural diversity with detailed alignments.
• A more efficient search capability was implemented using the Solr search server.
• The CATH v3.4 webpages offer enhanced access to protein structural and functional information.

Conclusions:

• CATH version 3.4 provides a richer, more informative resource for exploring protein structure-function relationships.
• The enhanced search functionality improves discoverability and accessibility of protein domain information.
• Continued updates to CATH ensure comprehensive coverage of protein fold space, incorporating novel structures.