[Elaine's spoke index]

Potential Sources of Domain Interaction Data

Summary

• if possible, it may be better for analyses to use biological unit (biologically relevant assembly or assemblies) rather than asymmetric unit
• if domain-domain interactions are not calculated directly from PDB entries (Peter's prerogative), these may be the most promising of the longer list below:
  • recently updated and some connection to Pfam domains: 3did, ProtCID, maybe 3D Complex
  • highly used by structural biologists, but may lack direct connection to Pfam domains: PISA
• I have not investigated the available downloads or licensing terms
• update 1/20/2021: Peter is looking at using EPPIC (Evolutionary Protein-Protein Interface Classifier): predicting the quaternary structure of proteins from crystal structures; Scooter suggests also looking at the ELM (Eukaryotic Linear Motif) resource
• update 1/27/2021: Peter compared EPPIC, 3did, ProtCID, and the latter may be the most promising if a bulk download is possible; he has contacted the authors (Dunbrack et al.)

Protein Interface Prediction or Databases

• PISA (Proteins, Interfaces, Structures and Assemblies)
  • see also jsPISA
• SPPIDER server: Solvent accessibility based Protein-Protein Interface iDEntification and Recognition
• InterProSurf server to find interface residues in protein complexes
• IBIS server: inferred biomolecular interactions, find interaction partners and binding sites
• ProMate server: Predicting potential protein-protein binding sites for unbound proteins

Domain Interaction Prediction or Databases

• 3did
  • over 14K high-resolution three-dimensional structural templates for domain-domain interactions based on Pfam version 32.0 and PDB version 2020_01
• ProtCID Common Interface Database
  • comprehensive, PDB-wide structural information on the interactions of proteins and individual protein domains with other molecules, including four types of interactions: chain interfaces, Pfam domain interfaces, Pfam-peptide interfaces and Pfam-ligand/nucleic acids interactions; based on Pfam version 32
• 3D Complex
  • hierarchical classification of protein complexes that describes similarities in structure, sequence, as well as topology of contacts of the constituent proteins, with domain definitions based on SCOP and Pfam
• PIFACE a clustered protein-protein interface database, allows search by Pfam domain
• Domprint domain-domain interaction prediction server ...haven't tried it
• DISPOT: a simple knowledge-based protein domain interaction statistical potential (2019) (available as source code, docker images, web server)

Old/Defunct

• DOMINE protein domain-domain interactions (last updated Sep 2010)
• DIMA3.0 comprehensive resource for functional and physical interactions among conserved protein-domains from iPfam and 3did plus predictions (last updated Sep 2010)
• PIBASE all protein structural interfaces extracted from the Protein Data Bank (2008) and PQS structure databases, with SCOP domain classifications
• iPfam: a database of protein family and domain interactions found in the Protein Data Bank (2013) (no longer exists)
• IDDI: integrated domain-domain interaction and protein interaction analysis system (2012) (no longer exists)
• InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes (2003) no longer exists)