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

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PepBDB is a complete database of biological peptide-mediated complex structures derived from the Protein Data Bank. It allows users to search/anlyze the database by combining a total of 12 options.

If users do not provide a value for an option, PepBDB will use the default parameter for database search. The default paramers for 12 options are as follows:
    Protein options:
  1. Protein sequence input/file: [all]
  2. Sequence identity for protein sequence search: [20%]
  3. Sequence identity for protein sequence clustering: [100%]
  4. Number of protein chains in the complex: [1-100]

    5. Peptide options:
  5. Peptide sequence input/file: [all]
  6. Sequence identity for peptide sequence search: [20%]
  7. Sequence identity for peptide sequence clustering: [100%]
  8. Peptide length in amino acids: [1-50]
  9. Whether or not to include peptides with nonstandard amino acids: [Yes]

    10. More options:
  10. Experimental method: [all]
  11. X-ray resolution: [10]
  12. Key words: [all]

The following is an example of the search results with the sample sequences:

PDB IDPeptideProteinContactResol.Mol.
Type		Protein
Seq ID		Peptide
Seq ID
1A1R C 16 108 0 A 1117 90 2.50 prot 100.0 100.0
2A4G B 22 159 0 ACD 1341 90 2.50 prot 99.3 100.0
2F9U B 23 168 0 ACD 1351 93 2.60 prot 99.3 100.0
2FM2 B 21 149 0 ACD 1341 93 2.70 prot 99.3 100.0
2GVF B 22 159 0 A 1353 92 2.50 prot 99.3 100.0
2OBO B 23 168 0 ACD 1357 99 2.60 prot 99.3 100.0
2OC8 B 22 159 0 ACD 1353 91 2.66 prot 99.3 100.0
2P59 C 16 108 0 A 1112 92 2.90 prot 99.3 100.0
2XNI C 21 149 0 ABD 1339 89 3.30 prot 99.3 100.0
3EYD B 22 159 0 A 1341 93 2.30 prot 99.3 100.0
2OBQ B 22 159 0 ACD 1335 88 2.50 prot 99.3 93.8
1N1L C 21 149 0 A 1337 89 2.60 prot 98.7 100.0
1RGQ C 22 159 0 ABD 1373 92 2.90 prot 98.7 100.0
1RTL C 21 149 0 ABD 1337 90 2.75 prot 98.7 100.0
2OIN C 16 108 0 A 1110 90 2.50 prot 98.7 100.0
2QV1 C 16 108 0 A 1113 91 2.40 prot 98.7 100.0
2XCF C 21 149 0 ABD 1334 89 2.48 prot 98.7 100.0
2O8M C 23 161 0 ABD 1357 94 2.00 prot 98.7 93.8

*Column explanations:

Col 1 - PDB ID; Col 2 - peptide chain ID; Col 3 - peptide length; Col 4 - number of atoms in peptide; Col 5 - peptide with nonstandard amino acid ? ( 1 means yes); Col 6 - protein chain ID; Col 7 - number of atoms in protein; Col 8 - number of atom contacts between peptide and protein; Col 9 - resolution (-1.00 means NMR structure); Col 10 - molecular type; Cols 11 & 12 - sequence identity with the query (0.0 means no sequence search).


The database is updated monthly.   Current version: 2020-03-18   
© Lab of Biophysics and Molecular Modeling, huanglab@hust.edu.cn