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About PepCyber:P~Pep
 
  • PepCyber :P~Pep is the largest public database of human protein-protein interactions mediated by phosphoprotein binding domains (PPBDs).
  • Current release: v. 1.2 (May 2010), includes 11,269 records of interactions between 387 PPBD proteins and 1,471 substrate proteins, curated from 4,852 published studies.
  • Please direct questions and comments to help@pepcyber.org.
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    References
     
  • Gong, W., Zhou, D., Ren, Y., Wang, Y., Zuo, Z., Shen, Y., Xiao, F., Zhu, Q., Hong, A., Zhou, X., Gao, X and Li, T. (2008) PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. Nucleic Acids Res , 36 , D679-683. [PubMed] [Full text]
  • Wan, J., Kang, S., Tang, C., Yan, J., Ren, Y., Liu, J., Gao, X., Banerjee, A., Ellis, L.B. and Li, T. (2008) Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection. Nucleic Acids Res . [PubMed] [Full text]
  •  
    Related databases
     
  • BOND (formerly BIND), by Unleashed Informatics.
  • DIP, developed at the University of California Los Angeles.
  • DOMINO, developed at the University of Rome Tor Vergata, Italy.
  • ELM, by Eukaryotic Linear Motif (ELM) consortium.
  • HPRD , developed at Institute of Bioinformatics, Bangalore, India and Johns Hopkins University.
  • Phospho.ELM, by Eukaryotic Linear Motif (ELM) consortium.
  • Scansite, developed at Massachusetts Institute of Technology.
  • STRING, by European Molecular Biology Laboratory (EMBL) and University of Zürich (UniZH)
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    Category. Types of record / interaction on the basis of whether the pertinent PPBD and/or the substrate peptide have been identified:
           - Category A: Both PPBD and the substrate peptide are identified;
           - Category B: PPBD is identified, the substrate peptide is not identified;
           - Category C: Specific PPBD is not identified, although the interaction involves a phophoprotein binding protein.

    Evidence. The evidence supporting an interaction between a PPBD protein and a substrate protein includes structural determination (by X-ray crystallography or NMR spectroscopy), peptide library experiments (e.g., phage display, oriented peptide library and mass spectrometry experiments), mutagenesis (usually followed by GST pull-down or yeast two-hybrid experiments), and sequence analysis.

    Index site. The index site refers to the position of the phosphorylated residue on the PPEP substrate protein, or the position of the central contact residue on non-PPEP substrate protein.

    Interaction. An interaction between a PPBD/PPBD protein and a substrate protein/peptide. One interaction may have been reported in multiple published studies, leading to multiple records.

    Non-PPEP substrate. A substrate peptide that is recognized by certain PPBDs, but does not contain phosphorylated residues.

    PPEP substrate. A phosphopeptide containing phosphorylated serine (pS), phosphorylated threonine (pT) or phosphorylated tyrosine (pY) that is known to bind a PPBD. All the substrate protein are named by using their Entrez Gene Name.

    PPBD. A protein domain which has affinity to phosphorylation sites in a protein or a peptide. A protein carrying one or more PPBDs is called a PPBD protein or PPBP. PPBDs selectively bind phosphorylated serines (pS's), phosphorylated threonines (pT's) and phosphorylated tyrosines (pY's) on a substrate protein. Presently, there are 10 known PPBDs in the human proteome. They are 14-3-3 , BRCT, C2, FHA, MH2, PBD, PTB, SH2 and WD-40 and WW. Some PPBDs bind PPEP substrates only, while others (e.g., WW and PTB) can bind both PPEP substrates and non-PPEP substrates.

    Protein name. The PPBD protein and substrate protein are named by using their Entrez Gene Name.

    Record. A literature account of an interaction between a PPBD/PPBD protein and a substrate protein/peptide.
           A record includes: information about the PPBD and PPEP: host protein, gene name, accession number, URLs to corresponding entries at NCBI RefSeq and Swiss-Prot databases, GO pathway, cellular location and disease terms, etc.; information about interactions: specific positions of PPBD and substrate peptides, the sequences containing interaction sites, interaction category, the supporting evidence of the interactions; link to the original article on PubMed.

    Substrate. The protein that bind a PPBD is termed a substrate protein, and the peptide on the substrate protein responsible for the binding (often 8-10 amino acides long) is termed a substrate peptide. A substrate of a PPBD can be either a PPEP substrate or a non-PPEP substrate.

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