ViennaPTM 3.0: Modify proteins with post-translational modifications

Table of Contents

• Overview
• Features
• Installation
• Usage
• Contributing
• License
• Logo and Trademarks
• Authors / Contributors

Overview

ViennaPTM is a software tool developed in the group of Prof. Bojan Žagrović at the Max Perutz Labs & University of Vienna. It enables the automated and chemically realistic introduction of PTMs into protein three-dimensional structures provided as PDB files.

ViennaPTM currently supports 256 different enzymatic and non-enzymatic PTMs and performs geometrically accurate placement of modifications at user-defined sites (see List of PTMs for a complete list).

Optionally, users can perform a subsequent energy minimization using the GROMACS molecular simulation package. This removes unfavorable steric orientations and makes the structure amenable to downstream processing.

ViennaPTM is designed to support structural and computational applications, such as molecular dynamics simulations and structural analysis. Force-field parameters are provided for the widely used GROMOS 45A3, 54A7, and 54A8 force-fields, with direct compatibility with GROMACS.

For full documentation, tutorials, and API reference, please visit the ViennaPTM Documentation.

Installation

For detailed installation instructions, refer to the Installation page, and for a step-by-step tutorial, consult the Tutorial page in the Documentation.

Create a new conda environment (optional)

conda create --name viennaptm python=3.11
conda activate viennaptm

Latest stable release

# Install the minimal package
pip install viennaptm

Install with development dependencies

# Install additional dependencies for 3D protein rendering
pip install viennaptm[render]

# Install additional dependencies for running tests
pip install viennaptm[test]

# Install additional dependencies for documentation generation
pip install viennaptm[docs]

Install from source

# Clone the repository
# SSH alternative: git@github.com:viennaptm/viennaptm.git
git clone https://github.com/viennaptm/viennaptm.git
cd viennaptm

# Install from source
# Add "-e" to install in editable (developer) mode
pip install .

Install GROMACS (optional)

GROMACS is required only if you wish to perform energy minimization on modified structures.

conda install conda-forge::gromacs

Usage

Entrypoint:

For more information, refer to the Entrypoint page in the documentation.

# Activate the conda environment
conda activate viennaptm

# Use the entrypoint to run ViennaPTM
viennaptm --input tests/data/1vii.pdb \
          --modify "A:50=V3H" \
          --output testoutput.pdb

API:

For more information, refer to the API page in the documentation.

modifier = Modifier()
structure = modifier.modify(
    structure=structure,
    chain_identifier="A",
    residue_number=50,
    target_abbreviation="V3H"
)

Contributing

Contributions from the community are highly welcome. Please consult the CONTRIBUTE.md before submitting changes, in order to help keep the code base maintainable, robust, and efficient.

License

• Code: Apache-2 (see code licence for more details)
• Resources [including modification libraries]: Attribution-NonCommercial 4.0 International (see library licence for more details)

Logo and Trademarks

The project name and logo are the property of the project maintainers. You may use the logo to refer to or link to this project, but not in a way that suggests endorsement or affiliation with derivative works without prior permission.

Authors / Contributors

• Sophie Margreitter - GitHub
• Christian Margreitter - GitHub
• Drazen Petrov - GitHub
• Jan Haschka - GitHub
• Bojan Žagrović - GitHub