ProtCAD

ProtCAD compiles and clusters protein assembly structures from the Protein Data Bank to identify and validate biologically relevant oligomeric assemblies observed across independent structural determinations.

Key Features:

• Assembly clustering: Clusters protein assembly structures derived from independent experimental determinations of homologous proteins in the Protein Data Bank (PDB).
• Coordinate files and PyMol scripts: Provides coordinate files and PyMol scripts for structure visualization and analysis.
• Cluster annotations: Provides annotations for each cluster to facilitate understanding and validation of assemblies.
• Ambiguity assessment: Addresses ambiguity in biological assembly determination, noting an estimated 10–15% of PDB entries have incorrect or unclear assembly annotations.
• Coverage of PDB entries: Covers approximately 60% of PDB entries in which assemblies are corroborated by at least two independent experiments.

Scientific Applications:

• Functional interpretation: Supports accurate interpretation of protein function by identifying biologically relevant oligomeric assemblies.
• Model training and prediction: Provides curated assembly clusters for training and benchmarking computational models, including deep learning methods, for assembly structure prediction.
• Assembly validation: Enables validation of biological assembly annotations through replication across independent structural determinations.
• Structural biology and bioinformatics: Serves researchers in structural biology and bioinformatics by supplying clustered assembly data derived from X-ray crystallography and cryo-electron microscopy.

Methodology:

ProtCAD compiles assembly coordinates from homologous protein structures in the PDB (including data from X-ray crystallography and cryo-electron microscopy) and clusters assemblies observed in multiple independent experiments, defining clusters supported by at least two independent determinations.