CATH

CATH classifies protein domain structures into homologous superfamilies to represent evolutionary relationships and enable structural and functional annotation of proteins.

Key Features:

• Curated classification (v3.4): Contains 128,688 domains organized into 2,386 homologous superfamilies and 1,233 fold groups.
• Automated and manual analysis: Integrates automated algorithms with manual expert analysis to define homologous relationships.
• Empirical and statistical evidence: Uses empirical and statistical evidence to validate classifications.
• Structural alignments: Provides detailed structural alignments of closely related and distantly related superfamily members annotated with functional insights and conserved residue details.
• Sequence and functional data: Presents sequence information and associated functional annotations for each superfamily.
• Structural genomics and transmembrane coverage: Incorporates structural genomics (SG) structures and transmembrane proteins to expand fold-space representation.
• Indexed search backend: Implements the Solr search server for indexed access to the dataset.

Scientific Applications:

• Evolutionary studies: Enables analysis of evolutionary relationships among protein domains and superfamilies.
• Functional annotation: Supports functional annotation of novel proteins based on structural and conserved-residue information.
• Protein fold-space exploration: Expands coverage of protein folds through inclusion of SG and transmembrane structures.
• Protein folding mechanisms: Provides comparative structural data to inform hypotheses about protein folding and fold stability.
• Structure-based function prediction: Facilitates prediction of protein function from structural similarity and conserved features.
• Drug discovery and molecular biology: Supplies structural and functional annotations useful for target identification and mechanistic studies.

Methodology:

Classification is produced by automated algorithms combined with manual expert analysis, supported by empirical and statistical evidence, structural alignments of close and distant members, and an indexed Solr search backend.