Data
Biopanning Data Bank (BDB) accepts peptide sequences selected from surface display random peptide libraries and other related information, such as the target, template, library and complex structure. Once public, data are welcome to be submitted to the database.
(1) Only peptides with available sequences are stored;
(2) Only peptides that are 40 amino acids or shorter are stored;
(3) Only peptides selected from surface display random peptide libraries are stored; those selected from phage display cDNA libraries, e.g. antibody phage display libraries, are excluded.
Users can choose one of the following two ways to submit your data to the BDB database.
(1) Using a default account
Submissions are made through a default BDB account. First, one would select the "Data" pull-down menu provided in the menu bar. Then you could choose the "Deposit Data" to login in as default account. You would go to the Add Data page and start to submit your data.
(2) Registering a BDB account
Submissions are made through a registered BDB account. Register a BDB account and login into BDB.
If you have login, you can click 
, go to the Add Data page and start to submit your data. After submitting data, you can manage the data and check the status of your data.
If you have any questions regarding the submission process contact us.
BDB is updated quarterly. Its content and tools can be accessed without any limitation and registration. All data in the BDB database has also been exported in xml files. Please click the icon below to download the data archive.
MimoBench is a benchmark dataset for mimotope-based protein-protein interaction study. There are 79 sets of biopanning data for protein-protein interactions with complex structure solved. Please click the icon below to download the benchmark data.
(1) Download data when browsing BDB
Data can be downloaded in xml files via selecting options "Download all data", "Download this page" or "Download selected". If users choose "Download all data", all data in one table will be downloaded. If users select "Download this page" option, data in the corresponding page will be downloaded. If users want to download specified entries, they should check the corresponding entries and choose "Download selected" option.
(2) Download data when searching BDB
Data can be downloaded in xml files via selecting options "Download this result" or "Download selected". If users choose "Download this result", all data that were found will be downloaded. If users want to download specified entries, they should check the corresponding entries and choose "Download selected" option.
To predict the protein interaction site based on mimotopes is a fascinating work for computational biologists. Quite a few methods and tools such as SiteLight, 3DEX, MIMOP, MIMOX, Mapitope, Pepsurf, Pepitope, Pep-3D-Search, and Episearch etc. have been developed in recent years. Thus benchmark datasets are desperately needed for tool evaluation and new algorithm development.
With the BDB database formerly known as MimoDB, it is convenient now for the community to produce benchmarks and customized data sets. In 2011, we constructed a dataset called MimoBench for mimotope-based protein-protein interaction study. The advanced search tool of the BDB database was used to find all biopanning data sets that have 3D structure of target–template complex. Corresponding biopanning data sets and related background information were then manually grouped, checked and compiled into a benchmark for programs that predict protein interaction site based on mimotopes. At that time, MimoBench had 23, 23 and 27 sets of data for antibody–antigen complex, receptor–ligand complex and other protein-protein complex, respectively.
Using MimoBench, we have performed a preliminary evaluation on Mapitope, Episearch and MimoPro by their default parameters. As all the tools tested could not manage template with multiple chains, four data sets were excluded from benchmarking. For unknown reason, MimoPro returned no results to another 10 data sets. Thus, the three tools were compared on the left 59 sets of data. For each case, the area under the curve (AUC) of each tool is computed as the arithmetic average value of its specificity and sensitivity. As shown in Figure 1, it seems that all the tools perform better with the antibody–antigen cases, and worse with receptor–ligand cases.
Figure 1. Benchmark Mapitope, Episearch and MimoPro with MimoBench. The string under the X-axis is the case tested. Each case has the format: PDB ID_BiopanningDataSet ID, where the left part is the PDB code of corresponding target–template structure, the right part is entry ID of the biopanning data set. (A) Antibody–antigen group, (B) receptor–ligand group and (C) other protein–protein interaction group.
At present, there are 24 sets of biopanning data for antibody-antigen interactions with complex structure solved, 24 sets of biopanning data with solved structures of corresponding receptor-ligand complex and 31 sets of biopanning data for other protein-protein interactions with complex structure solved. In total, it makes a benchmark with 79 sets of data for mimotope-based protein-protein interaction study. This dataset will be not only useful for benchmarking the existing tools, but also helpful for developing new and better algorithm to predict protein-protein interaction sites based on mimotopes.
