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CATH: an expanded resource to predict protein function through structure and sequence.

Natalie L Dawson1, Tony E Lewis2, Sayoni Das2

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The CATH-Gene3D database (version 4.1) now classifies over 53 million protein domains into 2737 superfamilies, doubling its previous scope. Updates include enhanced structural and sequence coverage and improved search functionalities for protein classification.

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Area of Science:

  • Structural bioinformatics
  • Genomics
  • Protein domain classification

Background:

  • The CATH-Gene3D database is a comprehensive resource for protein structure classification.
  • Previous versions provided a foundation for understanding protein domain evolution and function.
  • Continuous updates are essential to incorporate new structural and sequence data.

Purpose of the Study:

  • To report on the recent developments and release of version 4.1 of the CATH-Gene3D database.
  • To highlight significant improvements in data coverage, functional family expansion, and resource accessibility.
  • To detail advancements in automated domain classification and search functionalities.

Main Methods:

  • Expansion of structural and sequence data coverage.
  • Incorporation of new functional families within the CATH hierarchy.
  • Development of a support vector machine (SVM) for automated superfamily assignment.
  • Enhancement of web interface and download site functionalities.
  • Daily updates via the CATH-B resource for real-time domain assignment.

Main Results:

  • CATH-Gene3D version 4.1 includes over 300,000 domain structures and classifies over 53 million protein domains into 2,737 homologous superfamilies.
  • This represents a doubling of predicted protein domains compared to the previous version.
  • The CATH-B resource provides daily-updated classifications for over 100,000 additional protein domains.
  • Improved search tools facilitate alignment of query sequences against multiple sequence alignments.

Conclusions:

  • The latest CATH-Gene3D release significantly enhances protein domain classification resources.
  • Advancements in coverage, automated assignment, and search capabilities improve usability for researchers.
  • The database continues to be a vital tool for studying protein structure, function, and evolution.