CASTpFold

CASTpFold provides accurate and comprehensive identification and quantification of protein topography, including surface pockets, interior cavities, and cross channels, across Protein Data Bank structures and 183 million AlphaFold2-predicted structures.

Key Features:

• Expanded Database Coverage: Analyzes structures from the Protein Data Bank (PDB) and non-singleton representative AlphaFold2 structures, covering 183 million AF2 structures.
• Functional Pocket Prediction: Predicts functional pockets with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AlphaFold2-predicted structures.
• Pocket Similarity Search: Enables similarity search for surface pockets and protein-protein interface pockets.
• Topography Quantification: Locates, delineates, and measures geometric and topological properties including surface pockets, interior cavities, and cross channels.

Scientific Applications:

• Protein Function Annotation: Assigns GO terms and EC numbers to functional pockets of AlphaFold2-predicted structures to infer molecular function.
• Structural Comparison: Identifies similar pockets across surface and protein-protein interface regions for comparative structural analysis.
• Cavity and Channel Analysis: Characterizes interior cavities and cross channels to understand protein structure-function relationships.

Methodology:

CASTpFold builds upon the CASTp server framework and incorporates AlphaFold2 protein structures for topography analysis.