Therapeutic Peptide Design Database (TP-DB)

We make all the executables, python source codes, and prebuilt databases for the Therapeutic Peptide Design Database (TP-DB, https://dyn.life.nthu.edu.tw/design) available through GitHub (https://github.com/emmanuelsalawu/tp-db) and Zenodo (http://dx.doi.org/10.5281/zenodo.4628579). Please, refer to the README page on GitHub (https://github.com/emmanuelsalawu/tp-db) to know how to use the codes and the data.

1. sequences_helix_corrected_dec292017.fasta.zip

This file contains a list of the helical peptides in FASTA format. There is a need to first unzip it.

2. url_of_residue_residue_contact_information.xlsx

This file contains a list of the URLs linking to precomputed residue-residue contacts which is the number of amino acids in the protein within a given distance (in this case 7.3 Angstrom) from each of the amino acids.

3. indexes.db

This file contains the indexes of all the helical peptides in the database and helps in quickly knowing the amino acid patterns that are present in each of the helical peptides. It efficiently answers the question "what is the list of helical peptides that have a given amino acids pattern of interest?" This is a binary file and not readable as text. It is loaded by the executable file named "load_db_and_listen.exe".

4. seg_dbs.zip 

This contains the seg_dbs folder. The seg_dbs folder contains information that helps in knowing the exact location of a given amino acid pattern in the list of helical peptides that contain such a pattern. The information is used in conjunction with index.db (described above) for processing any given query. The files in this folder are binary and not readable as text. They are loaded by the executable file named "load_db_and_listen.exe" when they are needed.