An Information Portal to
Biological Peptide-protein complex structures
PepBDB collected all the biological complex structures of peptide-mediated protein interactions
with peptide lengths up to 50 residues
in the Protein Data Bank. A valid PepBDB record is a peptide-protein complex where the peptide
directly binds to at least one protein chain. PepBDB used the biological
units when searching the complexes meeting the criteria. The pdb files were carefully processed to obtain
cleaned peptide-protein complex structures and binding residues.
The database presents extensive information about biological peptide-mediated protein interactions.
PepBDB allows users to search the database by a variety of options including sequences and
interactively visualize the peptide-protein complex structures and interactions.
The database is updated monthly to include new data released in the PDB.
Current number of structures:
Wen Z, He J, Tao H, Huang SY. PepBDB: a comprehensive structural database of
biological peptide-protein interactions. Bioinformatics. 2018 Jul 6. doi:
Yan Y, Zhang D, Huang SY. Efficient conformational ensemble generation of
protein-bound peptides. J Cheminform. 2017;9(1):59.
- Yan Y, Wen Z, Wang X, Huang S-Y. Addressing recent docking challenges: A hybrid
strategy to integrate template-based and free protein-protein docking. Proteins
- Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov
IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
Laskowski RA, Swindells MB. LigPlot+: multiple ligand-protein interaction
diagrams for drug discovery. J Chem Inf Model 2011;51:2778-2786.
The database is updated monthly. Current version: 2020-03-18
© Lab of Biophysics and Molecular Modeling, firstname.lastname@example.org