The January 29, 2019 release offers the following new features: (Click here to download this version of the data )

The core data of the BDB database are sets of biopanning data and related information such as sequences, structures, targets, templates and libraries. Peptides are grouped into a set of biopanning data if they are from the same independent experiment. In the current release, 31,361 peptides grouped into 3,395 sets are collected from 1,604 published papers. Among the 31,361 peptides in BDB, 28,507 peptides appear only in one set of biopanning data; however, there are 1,833 peptides appearing in two or more sets of biopanning data for 4,687 times in total.


BiopanningDataSet:


Table 1: Biopanning data set distribution based on experimental method

      Experimental method        Number of set of biopanning data
Phage display (common panning)2158
Phage display (subtractive panning)657
Phage display (competitive panning)251
Phage display (in vivo)179
Phage display (subtractive panning, in vivo)10

Phage display (subtractive panning,competitive panning)

61
mRNA display (common panning)13
mRNA display (subtractive panning)5
mRNA display (competitive panning)6
Ribosome display (common panning)4
Ribosome display (subtractive panning)2
Ribosome display (competitive panning)3
Bacterial display (common panning)17
Bacterial display (subtractive panning)4
Bacterial display (competitive panning)5
Yeast display (common panning)          7          

 

Target:

 

There are 2039 different targets in the current version of BDB. Besides 185 target with undetermined sources and 164 targets with no sources (such as cellulose, polystyrene, microplate, etc.), most of the targets are from Homo sapiens (Human) and Mus musculus (Mouse). The source of some targets are a hybrid of two or more species.

 

Table 2-1: Target distribution based on target type

Target type        Number of target  
Organ and tissue107
Cell219
Virus22
Protein>Monoclonal antibody512
Protein>Polyclonal antibody208
Protein>Receptor88
Protein>Enzyme128
Protein>Others432
Nucleic acids30
Organic molecules or materials59
Inorganic molecules or materials130
Miscellaneous          92          

 

Table 2-2: Target distribution based on target source

       Target source               Number of target   
Homo sapiens(Human)704
Mus musculus(Mouse)516
Others391
Unknown190
None       165      

 

Template:

 

For most of the peptides in the BDB database, their templates are not or even can not be determined. Thus, there are only 562 templates identified.

 

Table 3-1: Template distribution based on template type

      Template type        Number of template 
Cell12
Virus21
Protein>Monoclonal antibody9
Protein>Polyclonal antibody4
Protein>Receptor36
Protein>Enzyme42
Protein>Others354
Nucleic acids2
Organic molecules or materials57
Inorganic molecules or materials6
Miscellaneous4
Organ and tissue2

 

Table 3-2: Template distribution based on template source

   Template source     Number of template  
Homo sapiens(Human)205
Mus musculus(Mouse)20
Others260
Unknown51
None       16        

 

Structure:

 

Table 4: Complex structure and related sets of biopanning data

  Complex    Target-template Target-peptideIn Total 
Structure number27639315
Related sets of biopanning data17810188*
Related targets69877*
Related templates636  69*  

 

Library:

 

In the current version of the BDB database, there are 498 phage libraries or library pools.

 

Table 5-1: Library distribution based on randomness

         Library randomness            Number of library  
Completely random327
Semi-random       169      

 

Table 5-2: Library distribution based on topology

 Library topology  Number of library 
Linear280
Circular169
Mixture(linear, circular)

                41