Are you tired of using visualization software, or full blown suites just to separate protein chains / ligands ? Are you tired of organizing the mess of molecules into separate folders ?

PDBaser does this for you !

What does it do ?

PDBaser reads raw .pdb and .ent files as downloaded from the pdb, extracts pure protein chains and heteroatoms (ligands and others) and removes water molecules, and then saves everything in a directory named as the original input filename.

Who is this for ?

This tool is perfect for RMSD reliability test preparation, where a large number of proteins and their ligands are needed. It can also help people who are not very accustomed to command line interfaces, and aren't willing to pay a (usually high) premium for other software.

Installation

Windows

For Windows users, PDBaser has a precompiled version, it can be found in the releases category, and can be installed on windows 7 SP1 / 8 / 8.1 / 10 and only requires Microsoft visual C++ 2015 x86.

Linux / MacOS and other Unix / Unix-like systems

There are 2 possible ways to run PDBaser in this case :

1. Using Wine

   The quickest way to get PDBaser running on those systems is by using Wine (Tested on Wine 6.0.1, works only on a 64bit prefix for some reason),

   • 1 - Download and install the windows msi package and install it.
   • 2 - open a terminal window where you installed PDBaser and run wine PDBaser_GUI.exe.

2. Building from source

   PDBaser is not OS dependant, and will probably run on any operating system provided the environment is correctly setup. However, since software distribution on Linux is a nightmare, and i do not have a mac system to package PDBaser for, you will have to either use Wine, or deal with setting up the environment from scratch.

   • 1 - First, you need a working python environment with support for Tkinter (i'm looking at you, Arch Linux)
   • 2 - Install BioPython and Pygubu from pip (pip install biopython / pip install pygubu)
   • 3 - You need to build openbabel 3.1.1 with depiction support (Cairo) and python bindings from source, and then install it from pip (pip install openbabel==3.1.1).

   If everything is setup correctly, running GUI/Build/PDBaser_GUI.py should work.

Features

• Folder organization (Outputs are organized in a single folder named as the pdb file name).
• Support for compressed pdb / ent files.
• 2D Depiction and PNG/SVG output.
• Outputs residues in most popular formats (pdb, sdf, mol2, smiles).
• Multiple residue extraction at once is possible, chain only extraction with no residues is also possible.
• Hydrogen generation for extracted residues is available (Except for SMILES format).
• Support for downloading proteins from the PDB directly.

Limitations

• No metadata extraction (Header, comments etc ...), only atom 3D poses with the molecule code in the PDB.
• Only .pdb / .ent inputs and their compressed (.gz) form are supported, this is done by design as most proteins come only in pdb and ent formats, however residue outputs can have different formats (pdb, mol2, sdf, smiles).
• there is a known bug where extracting a ligand in SMILES format does not generate a name for it, i'm gonna fix it as soon as i finish some work on my studies.

Downloads

For Windows x86/x64 : A binary setup is available in releases section.

For Unix/Unix-like(Linux/MacOS etc..) : Source is available in releases section, although i recommend installing the windows version and using it through Wine.

Citations

PDBaser relies on Biopython's BIO.PDB module, openbabel's pybel module and OASA.

BIO.PDB : Hamelryck T and Manderick B (2003) PDB file parser and structure class implemented in Python. Bioinformatics, 22, 2308-2310

openbabel's pybel : O'Boyle, N.M., Morley, C. & Hutchison, G.R. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. Chemistry Central Journal 2, 5 (2008).

If this software helped you making a scientific publication, please cite it using the citation below :

M. A. Abdelaziz, “PDBaser, A python tool for fast protein - ligand extraction”, https://github.com/mimminou/PDBASER

Command line (Deprecated)

NOTE : CLI version is a very early release and is now DEPRECATED, and probably won't be supported anymore.

for this module to work, you need at least python 3.6.5 as well as Biopython.

from the date i'm writing this, i've been experiencing some issues regarding Biopython when running python 3.9, therefore i suggest users to download any iteration of python from 3.6.5 to 3.8.5 instead.

You can download and install python from the official website (3.6.5 recommended).

Biopython can be installed from pip.

Usage

Very straightforward, all you have to do is put this script in the folder containing the PDBs that need to be treated, run it from command line / terminal then follow instructions for each iteration.

There exists only 3 commands :

• SKIP : command that skips the mentioned step.
• Inserting data : normal usage.
• Leaving blank field : will either default to chain A or extract all residues in the selected chain, depending on where the user left the input blank.