StrIDR: Structures of Intrinsically Disordered Regions

StrIDR is a database of IDRs, confirmed via experimental or homology-based evidence, that are resolved in experimentally determined structures.
Existing databases provide extensive information for IDRs at the sequence level. However, only a tiny fraction of these IDRs are associated with an experimentally determined protein structure. Moreover, the disordered region of interest could be unresolved even if a structure exists.
StrIDR is expected to be useful for gaining insights into the dynamics, folding, and interactions of IDRs. It may provide structural data for computational methods to studying IDRs including molecular dynamics (MD) simulations and machine learning (ML).

Publication and Website

Kartik Majila, Shruthi Viswanath, StrIDR: a database of intrinsically disordered regions of proteins with experimentally resolved structures., at DOI: https://doi.org/10.1101/2024.08.22.609111.

StrIDR webserver: https://isblab.ncbs.res.in/stridr

Dependencies:

• See requirements.txt for Python dependencies

Directory structure

1. Database : contains the input files for database creation and the database.
2. scripts : contains all the scripts used for creation of the database.

Creating StrIDR

Obtain data files from disorder databases and datasets

IDR Databases	Download URL	File Format	Date of Access
DIBS	https://dibs.enzim.ttk.mta.hu/downloads.php	XML	19 Jul, 2024
MFIB	https://mfib.pbrg.hu/downloads.php	XML	19 Jul, 2024
FuzDB	https://fuzdb.org/browse/	TSV	19 Jul, 2024
DisProt	https://disprot.org/download	TSV	19 Jul, 2024
IDEAL	https://www.ideal-db.org/download/archive/	XML	19 Jul, 2024
MobiDB	https://mobidb.bio.unipd.it/#/swagger	used API	19 Jul, 2024
PDBtot and PDBcdr	https://doi.org/10.1016/j.jmb.2020.02.017	XLSX	19 Jul, 2024

MobiDB entries are downloaded using the MobiDB API.

Add the downloaded data files to the ./Database/raw/ directory. The file names must match those specified in 1_download_databases.py.

Creating input files for StrIDR construction

python 1_download_databases.py -c CORES

CORES - number of cores to parallelize on (we used 10). This script generates the following files that are used by the downstream script:

1. Merged_Uniprot_IDs.txt : file containing UniProt accessions obtained from the aforementioned databases and datasets.
2. Merged_PDB_IDs.txt : txt file containing PDB IDs for all UniProt accessions.

Creating StrIDR database

python 2_create_database_dataset_files.py -c CORES

CORES - number of cores to parallelize on (we used 200).

Move files to the website directory

python move_to_web_dir.py

Note

Please check network connectivity before running the scripts or use lesser CORES in case of a high server request failure.

Populate the SQL database and make migrations

cd ../website/dbsite/
python populate.py
python manage.py migrate
python manage.py makemigrations database
python manage.py migrate

Information

Author(s): Kartik Majila, Shruthi Viswanath

Date: August 22, 2024

License: CC BY-SA 4.0 This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Parallelizeable: Yes

Publications: Majila, K. and Viswanath S. StrIDR: a database of intrinsically disordered regions of proteins with experimentally resolved structures. DOI: https://doi.org/10.1101/2024.08.22.609111.