Project framework

ProtCID fuses information from a large set of data compiled from various sources: protein structure data from the Protein Data Bank (PDB), protein family architectures from Pfam, biological assemblies from the PDB and Protein Interfaces, Surfaces and Assemblies (PISA), the residue mapping between UniProt and PDB sequences from SIFTs , and alignment data generated from PISCES , protein sequence information from the Universal Protein Resource (UniProt) . Software used in ProtCID are: FATCAT, HMMER, PsiBlast and HHblits.

Web site framework

ProtCID can be queried by input PDB code, one or two Pfams, one or two protein sequences and one or multiple UniProts. Pfams, Clans, Pfam pairs, peptide binding Pfams, and ligands can be also browsed in the ProtCID web site. Coordinates, sequences and clusters can be downloaded.