PepX: a structural database of protein-peptide complexes

Application of the PepX database

Vanhee, P., F. Stricher, et al. (2009). "Protein-peptide interactions adopt the same structural motifs as monomeric protein folds." Structure, August, 2009. 

The video below demonstrates the algorithm used to reconstruct protein-peptide binding sites.

3D complex databases

Database	Scope	Reference
	3D structures of domain-domain and domain-peptide interactions	Stein A, Panjkovich A, Aloy P. (2009). 3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res. D300-4.
	PDB structures and their associated ligands	Gonzalo Lopez, A. Valencia, and M. Tress. FireDB - a database of functionally important residues from proteins of known structure Nucl. Acids Res. 2007 35: D219-D223
	Hormones and receptors	Rashid M, Singla D, Sharma A, Kumar M and Raghava GPS (2009): Hmrbase: a database of hormones and their receptors. BMC Genomics 10(1): 307.
	T cell receptor/peptide/MHC interactions	Tong JC, Kong L, Tan TW, Ranganathan S (2006). MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions. Appl Bioinformatics 5(2):111-4.
	Small molecular ligands bound to larger biolomocules	Jae-Min Shin and Doo-Ho Cho (2005) PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. Nucleic Acids Res. 33, D238-D241.
	Protein-ligand complexes with binding energies, Tanimoto ligand similarity scores and sequence similarities	Puvanendrampillai D, Mitchell JB (2003). L/D Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes. Bioinformatics 19(14):1856-7.
	Protein cognate ligands for enzyme structures	Bashton M, Nobeli I, Thornton JM (2008). PROCOGNATE: a cognate ligand domain mapping for enzymes.Nucleic Acids Res. D618-22.
	Descriptions of PDB ligand structures	Michalsky E, Dunkel M, Goede A, Preissner R. (2005). SuperLigands - a database of ligand structures derived from the Protein Data Bank. BMC Bioinformatics 6:122.
	Calculating packing densities of proteins and ligands	Rother K, Hildebrand PW, Goede A, Gruening B, Preissner R. 2009. Voronoia: analyzing packing in protein structures. Nucleic Acids Res. (Database issue), 37, D393-5.