PepBDB -- a structural database of biological peptide-mediated interactions

Huang lab       Home       Browse      Search      Help & example      Download     



PepBDB

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:   12241
Browse Search Help

References:
  1. Wen Z, He J, Tao H, Huang SY. PepBDB: a comprehensive structural database of biological peptide-protein interactions. Bioinformatics. 2018 Jul 6. doi: 10.1093/bioinformatics/bty579.
  2. Yan Y, Zhang D, Huang SY. Efficient conformational ensemble generation of protein-bound peptides. J Cheminform. 2017;9(1):59.
  3. 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 2017;85:497-512.
  4. Huang S-Y, Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008;72:557-579.
  5. 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.
  6. 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: 2019-02-20   
© Lab of Biophysics and Molecular Modeling, huanglab@hust.edu.cn