ProtCID

[1][5] Its main goal is to identify and cluster homodimeric and heterodimeric interfaces observed in multiple crystal forms of homologous proteins.

[6] A common interface in ProtCID indicates chain-chain or domain-domain interactions that occur in different crystal forms.

All protein sequences of known structure in the Protein Data Bank (PDB)[7] are assigned a ”Pfam chain architecture”, which denotes the ordered Pfam[8] assignments for that sequence, e.g. (Pkinase) or (Cyclin_N)_(Cyclin_C).

ProtCID provides an independent check on publicly available annotations of biological interactions for PDB entries.

ProtCID also contains interface clusters between protein domains and peptides, nucleic acids, and ligands.

Example of cluster of similar interfaces of homologous proteins identified by ProtCID -- similar homodimers of ERBB kinases (EGFR, ERBB2, ERBB4) associated with kinase activation. [ 2 ] [ 3 ] [ 4 ] Each monomer is colored from blue to red from N to C terminus. ProtCID provides PyMol scripts for each cluster to produce similar images.