The December 30, 2020 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, 33,097 peptides grouped into 3,562 sets are collected from 1,700 published papers.Among the 33,097 peptides in BDB, 28,045 peptides appear only in one set of biopanning data; however, there are 1,957 peptides appearing in two or more sets of biopanning data for 5,052 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)2253
Phage display (subtractive panning)685
Phage display (competitive panning)280
Phage display (in vivo)194
Phage display (subtractive panning, in vivo)11

Phage display (subtractive panning,competitive panning)

64
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 2076 different targets in the current version of BDB. Besides 198 targets with undetermined sources and 169 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 tissue117
Cell225
Virus22
Protein>Monoclonal antibody522
Protein>Polyclonal antibody233
Protein>Receptor93
Protein>Enzyme132
Protein>Others459
Nucleic acids30
Organic molecules or materials65
Inorganic molecules or materials140
Miscellaneous         104         

 

Table 2-2: Target distribution based on target source

       Target source               Number of target   
Homo sapiens(Human)755
Mus musculus(Mouse)538
Others481
Unknown201
None   181   

 

Template:

 

For most of the peptides in the BDB database, their templates are not or even can not be determined. Thus, there are only 564 templates identified.

 

Table 3-1: Template distribution based on template type

      Template type        Number of template 
Cell12
Virus22
Protein>Monoclonal antibody10
Protein>Polyclonal antibody5
Protein>Receptor37
Protein>Enzyme43
Protein>Others368
Nucleic acids2
Organic molecules or materials59
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)209
Mus musculus(Mouse)21
Others275
Unknown52
None       18        

 

Structure:

 

Table 4: Complex structure and related sets of biopanning data

  Complex    Target-template Target-peptideIn Total 
Structure number27739316
Related sets of biopanning data17110189*
Related targets70878*
Related templates646  70*  

 

Library:

 

In the current version of the BDB database, there are 503 phage libraries or library pools.

 

Table 5-1: Library distribution based on randomness

         Library randomness            Number of library  
Completely random333
Semi-random       174      

 

Table 5-2: Library distribution based on topology

 Library topology  Number of library 
Linear297
Circular180
Mixture(linear, circular)

                            49