protcid

is a Data Source.

The Protein Common Interface Database (ProtCID) provides comprehensive, PDB-wide structural information on protein interactions, identifying and clustering interfaces observed in multiple crystal forms of homologous proteins.

Domains

proteomics, chemistry and biochemistry, biological systems

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Homepage

protcid

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Product Summary

Contacts

Qifang Xu

Roland L. Dunbrack Jr

Fox Chase Cancer Center

Products

From this Resource
ID Name URL Category Format Description
protcid.database ProtCID Database ❔ Product ❔ Database containing protein-protein i...
protcid.site ProtCID Web Interface search.aspx GraphicalInterface ❔ Web interface for searching and visua...
From other Resources
ID Name URL Category Format Description
spoke.graph SPOKE Graph ❔ GraphProduct ❔ The SPOKE knowledge graph containing ...

Details

The Protein Common Interface Database (ProtCID) contains comprehensive, PDB-wide structural information on the interactions of proteins and individual protein domains with other molecules. The database is based on Pfam v34 and identifies common interfaces across different crystal structures.

ProtCID includes four types of interactions:

  1. Chain-chain interfaces
  2. Pfam domain-domain interfaces
  3. Pfam-peptide interfaces
  4. Pfam-ligand/nucleic acids interactions

The main goal of ProtCID is to identify and cluster homodimeric and heterodimeric interfaces observed in multiple crystal forms of homologous proteins, and interactions of peptides and ligands in homologous proteins. Such interfaces and interactions, especially of non-identical proteins or protein complexes, have been associated with biologically relevant interactions.

ProtCID provides an independent check on publicly available annotations of biological interactions for PDB entries, and can be used to identify biological protein complexes, especially weak interactions like asymmetric homodimers. The clusters of Pfam-peptide and Pfam-ligand interactions can be used to develop hypotheses for the structures of other protein families within the same superfamilies (Clans).

The database can be searched using PDB codes, PFAM IDs or accession codes, protein sequences, or UniProt IDs. It also allows browsing of Pfams, Clans, Pfam-Pfams, peptide-Pfams, and ligands in the PDB.

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Created: May 28, 2025 | Last modified: October 31, 2025