A reply to what do databases such as CATH and SCOP offer that PDB lacks

Reply to what do databases such as CATH and SCOP offer that PDB lacks?. The Protein Data Bank (PDB) is an international archive of protein, nucleic acids, and other assembly’s 3D structures (PDB, 2020). It is considered the primary source for protein structures used for research and education (PDB, 2020). The data maintained in this database includes descriptions of crystal and chemical structure and atomic coordinates (Pevsner, 2015). PDB does not provide hierarchical classification of their protein structures. Databases such as CATH and SCOP are used to supplement PDB for research regarding protein structures.

CATH is named for their ability to classify proteins based on their class, architecture, topology, and homology (Knudsen & Wiuf, 2010). CATH provides a hierarchical classification of proteins based on their sequence information as well as their structural and functional properties (Knudsen & Wiuf, 2010). CATH determines the hierarchical classification based primarily on the secondary structure domains (Pensver, 2015). CATH also provides classification of the sub-sequences of proteins that may fold and function independently from the main structure of the protein (Knudsen & Wiuf, 2010).

SCOP (Structural Classification of Proteins) database was created with the goal of providing detailed descriptions of the structural and evolutionary relationship between all proteins, based on their known structure (Fox, Brenner, & Chandonia, 2014). While also providing information about close relatives of any protein, it includes a framework for future research and classifications for their large collection of known protein folds (Fox, Brenner & Chandonia, 2014). SCOP is the more widely used than CATH as its class level classifications includes two mixed alpha-beta classes, α+β and α/β (Knudsen & Wiuf, 2010). SCOP uses the ASTRAL compendium to provide sequence and coordinate files for all SCOP and sequences for the Protein Data Bank (PDB) that are classified in SCOP (Fox, Brenner & Chandonia, 2014). Once a hierarchy is established for each protein domain, the database links the domain to its unique PDB entry (Pensver, 2015).

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