PDBASER

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Protein preparation for MD, made faster and easier !

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![mainicon](https://raw.githubusercontent.com/mimminou/PDBASER/main/GUI/icon.png)

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 is the right tool 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 (optionally) removes water molecules, then saves everything in a directory named as the original input filename.
You can also use it to generate and extract a binding site provided there is a ligand in a cavity in the protein file.

# Who is this for ?

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

# 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.
- Binding Site Extraction is available for up to 12Å in radius from a selected residue.
- Water extraction in chains and binding site is available.
- Protonation and titration states predictions for proteins and binding sites using PROPKA.  
- Hydrogen generation for extracted residues is available.
- Support for downloading proteins from the PDB directly (files are saved in input directory).
- Powerfull batch extraction mode through CLI.

![Screenshot](https://raw.githubusercontent.com/mimminou/PDBASER/main/GUI/pdbaser.PNG)

# Installation

#### Windows

For Windows users, PDBaser has a precompiled version, it can be found in the releases section, and can be installed on windows 7 SP1  or newer, and only requires Microsoft visual C++ 2015 x86, which is embedded in the setup. ( For Windows 7 Users : Service Pack 1 with update KB3063858 Must be installed in order for PDBaser to run )

#### Linux / MacOS and other Unix / Unix-like systems

There are 3 possible ways to run PDBaser in this case :

1. **Using Wine**

The quickest and easiest way to get PDBaser running on those systems is by using Wine (Tested on Wine 6.0.1 +) or a wine manager software like Bottles.
    
    - 1 - Download and install the windows setup package and install it.
    - 2 - open a terminal window where you installed PDBaser and run `wine pdbaser.exe` (or `wine PDBaser_GUI.exe` if release is older than 2.0).

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 still somewhat a new concept for me, 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 3.6+ environment with support for Tkinter and PILLOW.
    - 2 - Install BioPython and Pygubu from pip (`pip install biopython`, `pip install pygubu`)
    - 3 - You need to install openbabel 3.1.1 with python bindings (pybel), or directly build openbabel 3.1.1 with SWIG and python bindings from source ( follow [this](http://openbabel.org/docs/UseTheLibrary/PythonInstall.html) ).
    - 4 - Install the OASA library, obtainable from pip ( `pip install oasa3` )
    - 5 - Install PDB2PQR ( `pip install pdb2pqr` )(which in turn will automatically install PROPKA, both are needed)

If everything is setup correctly, running GUI/Build/pdbaser.py from terminal should work, if not, email me at abdz.amine@gmail.com or open an issue in the repository.
    
    If PDBaser warns you about pybel not being available or is available but only with partial support, check your environment variables for BABEL_LIBDIR.
    
3. **Building Binaries**

If you need to build binaries, and do not want to install the precompiled binaries from the releases section, clone the repository, build all the dependencies ( see previous section ), then using some Python compiler or a python freezer, build with main executable being pdbaser.py.
    
    If you Use Nuitka, a Nuitka_script.txt file is provided in PDBaser/GUI/Build with a bunch of command arguments in there, they are specific to my machine so adapt them as you see fit.

If you compile PDBaser for Windows, copy the content of your openbabel library into the build folder under /obabel/openbabel.

### 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).
- Extracting a ligand in SMILES format does not generate a name for it, this is a known bug, I will probably fix it if it raises issues.
- PDBaser does not handle well structures that are composed of multiple models, and tries to skip non peptidic chains, so try to avoid them as much as possible.

### Roadmap

From most to least important :
- Add cif (mmcif) support.
- Add binding site AA extraction to seperate files (Each AA on it's seperate .pdb file, user requested feature).
- Packaging binaries for Linux (Maybe through flatpak).

# Downloads

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

For Unix/Unix-like : Source is available in releases section, although I recommend installing the windows version and using it through Wine.

# Citations

PDBaser is based on Biopython's BIO.PDB module, openbabel's pybel module, the OASA library and PDB2PQR.

BIO.PDB : Hamelryck T and Manderick B (2003) PDB file parser and structure class implemented in Python. [*Bioinformatics*, 22, 2308-2310](http://dx.doi.org/10.1093/bioinformatics/btg299)

Openbabel + 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).

PDB2PQR (+ PROPKA ) : https://github.com/Electrostatics/pdb2pqr

**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
Starting from PDBaser 2.0, command line functionality is back with batch operations and arguments support.
However, it is still in testing phase and should be used carefully.

### Usage

Invoke pdbaser by passing arguments:

`pdbaser -i [INPUT] -o [OUTPUT]`

**Help** :

Running `pdbaser -h` will show a help message.

-h, --help            shows a help message and exit

**Required arguments:**

`-i INPUT_DIR, --input INPUT_DIR` : Input directory for pdbs, if a file is specified instead, it will only treat that file and exit.
  
`-o OUTPUT_DIR, --output OUTPUT_DIR` : Output directory for processed files ( Must be an existing directory )

**Example** :

`./pdbaser.exe -i C:\Users\USER\Desktop\zz\IC50MOLES\cli_test -o ./exp/ -r -bs 8 -pbs -ff CHARMM -ph 8 -w`

**Optional arguments**

A list of optional arguments can be found in USAGE.txt (https://github.com/mimminou/PDBASER/blob/main/GUI/Build/USAGE.txt)

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