1 Installation guide

1.1 Download stand-alone package

git clone https://github.com/ShutaoChen97/PDB-BRE.git

or click here.

1.2 Operating systems compatibility and requirements

PDB-BRE is programmed based on Python 3.8. For the convenience of researchers, PyInstaller has been used to freeze the PDB-BRE source code into several separate executables so that it can run directly on platforms without Python installed.

The PDB-BRE should be compatible with any Windows- and Linux-based operating system, but in some cases some additional data may be required for analysis input, see below.

If a problem occurs during the installation or if PDB-BRE is not running properly, please read the information reported below about the possible problems that may occur with PDB-BRE or contact us (stchen@bliulab.net).

1.2.1 Network connection

PDB-BRE needs to automatically obtain the 3D structure data of the analyzed protein structure from RCSB PDB database and EMBL-EBI database, so please make sure the network connection is normal before running PDB-BRE.

Connectivity tests (ping or browser access) can be performed at the following link:

For RCSB PDB : https://www.rcsb.org/

For EMBL-EBI : https://www.ebi.ac.uk/pdbe/

1.2.2 UniProt mapping database

In some studies, to realize the unified input of protein sequences, it is necessary to map the protein chains in the input PDB format files. In PDB-BRE, the Reviewed (Swiss-Prot) resource in UniProtKB is used for mapping by default (./uniprot_sprot.fasta), and users can download other resources and manually change the relevant parameters.

Other UniProt data sets that can be used for protein chain mapping are detailed in: https://www.uniprot.org/help/downloads.

1.2.3 Windows PowerShell (for Windows)

PDB-BRE uses the tqdm package in Python to display progress information about some executable files, which may cause print exceptions in Windows’s command (CMD). Therefore, for the Windows-based operating system, we recommend using Windows PowerShell to run PDB-BRE’s executable.

Windows PowerShell is available for free through the Microsoft Store or as a download at the following link: https://github.com/PowerShell/PowerShell.

1.3 Package installation

1.3.1 For Liunx

To install PDB-BRE, unarchive the downloaded tarball:

tar -xvzf PDB-BRE_1.0.0.tar.gz

Then, move the four executable files in the ‘Linux’ folder to the <INSTALL_DIR> directory.

Change directory to the resulting folder:

cd PDB-BRE_1.0.0

1.3.2 For Windows

To install PDB-BRE, unarchive the downloaded tarball (PDB-BRE_1.0.0.tar.gz). Then, move the four executable files in the ‘Windows’ folder to the <INSTALL_DIR> directory.

Use Windows PowerShell to enter the decompressed file directory.

cd <INSTALL_DIR>

1.3.3 For OS X

To install PDB-BRE, unarchive the downloaded tarball (PDB-BRE_1.0.0.tar.gz). Then, move the four executable files in the ‘OS X’ folder to the <INSTALL_DIR> directory.

Enter the decompressed file directory.

cd <INSTALL_DIR>

1.4 Installation test

To test the software installation, enter the following command:

cd <INSTALL_DIR>
./PDB-BRE-InterPair -h

If prompted to report an error, check to make sure the executable has been moved to <INSTALL_DIR>.