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. 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. Supplementary_Data_1.zip

This file contains the helices in the TP-DB alongside the helical propensity, average residue contact, sequence length, and the URL to the 3D structure of each of the helices.

Each row contains information of each helix, such as the PDB accession code, chain ID, type of helix, the range of residue IDs, amino acids sequence, helical propensity, contact number, and a hyperlink (URL) for downloading each helix in PDB format. 

Each of the helices is named in the following format PDBID_ChainID_HelixType_PositionOfFirstResidue_PositionOfLastResidue. For example, the helix named 3ufx_F_1_73_87 means that this helix is from PDB 3ufx, chain F, is of type "Right-handed alpha" helix, starts at residue 73, and ends at residue 87. 

The types of helices and the associated class numbers are available in PDB's documentation (https://www.wwpdb.org/documentation/file-format-content/format33/sect5.html) and are summarized below. 

                                     CLASS NUMBER
TYPE OF  HELIX                     (COLUMNS 39 - 40)
--------------------------------------------------------------
Right-handed alpha (default)                1
Right-handed omega                          2
Right-handed pi                             3
Right-handed gamma                          4
Right-handed 3 - 10                         5
Left-handed alpha                           6
Left-handed omega                           7
Left-handed gamma                           8
2 - 7 ribbon/helix                          9
Polyproline                                10

2. helical_sequences.zip

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

3. 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.

4. 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".

5. 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.

The remaining files are used by the TP-DB web server and (can be read) by the codes provided on GitHub (https://github.com/emmanuelsalawu/tp-db). The users will not need to open those files directly. Additional information can be found on the Github page.