November 15, 2011 (Vol. 31, No. 20)


Strong Points: Clean organization, easy to browse
Weak Points: Nothing major


One need not think outside the box to gain a new perspective on proteins. Rather, simply think inside the secondary structure. That is, instead of browsing protein structures by name, one can explore the myriad structures via structural characteristics, thanks to CATH. This protein structure classification system (which stands for Class, Architecture, Topology, and Homologous superfamily) uses the C-A-T-H parameters to hierarchically classify the proteins in the Protein Data Bank (PDB). One can search the database by PDB codes/chains, CATH domain codes/classification codes, or by FASTA sequence. Alternatively, one can spend a great deal of time browsing the entries by secondary structure classes: mainly alpha helices, mainly beta sheets, mixed alpha/beta, or few secondary structures. These, in turn, lead to architectural features like the “alpha horseshoe” and the “orthogonal bundle”, and “down the rabbit hole you go.” Happy travels!

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