Bio2byte :: Molecular dynamics utilities

by David Bickel and Wim Vranken

This repository contains an assembly of templates, scripts, and Jupyter notebooks for running and analyzing large-scale MD simulations.

Contents

├── notebooks/                              # Jupyter notebook templates
│   ├── bmrb_comparison.ipynb
│   ├── build_peptides.ipynb
│   ├── constava_adjacent.ipynb
│   ├── constava.ipynb
│   ├── dihedral_timeseries.ipynb
│   ├── dssp_summary.ipynb
│   ├── hbond_plots.ipynb
│   ├── pca_comparison.ipynb
│   ├── pca_replica_correff.ipynb
│   ├── ramachandran.ipynb
│   ├── rama_effect_propagation.ipynb
│   ├── rama_rmsd.ipynb
│   └── README.md
├── slurm/                                  # SLURM script templates
│   ├── conformational_variability.slrm
│   ├── dihedral_pca.slrm
│   ├── dihedrals.slrm
│   ├── mediated_hbonds.slrm
│   ├── prepare_mdsystems.slrm
│   ├── process_trajectories.slrm
│   ├── replica_correlation.slrm
│   └── README.md
├── templates/                              # MD simulation templates
│   ├── forcefields/
│   ├── template_ff99sb/
│   └── README.md
├── src/                                    # Python code for analyses
│   └── bio2byte/mdutils
└── README.md (this file)

Building and installing the repository

If you just want to use the templates or copy some code from the notebooks, there is no need to install the package. Just go through the directories and copy what you need.

If you though, want to use the prewritten scripts, SLURM scripts and notebooks as they are, you will need to build this package and install it. Here, is how:

# Create a virtual environment (optional but recommended)
python -m venv mdutils
source mdutils/bin/activate

# Get a copy of the repository on your local machine
git clone https://github.com/Bio2Byte/bio2byte-mdutils.git

# Enter the repository
cd bio2byte-mdutils

# Build the repository
make build

# Install the repository
make install

Installing the repository will give you access to a couple of commands to help you with your MD analyses (also see Usage):

Command	Description
mdutils-process-trajectory	Processes MD trajectories (center protein, PBC image, remove solvent)
mdutils-hbonds-wrapper	Calculates solute hydrogen bonds as well as solvent mediated hydrogen bonds
mdutils-hbonds	Calculates hydrogen bonds in a MD trajectory
mdutils-centroid	Estimates the centroid structure of a MD ensemble
mdutils-dihedral	Calculates phi/psi dihedral angels in a MD ensemble
mdutils-dihedral-pca	Performes a PCA on the phi/psi backbone dihedrals
mdutils-replica-correlation	Calculates correlation coefficients between replicas along N principal components
mdutils-ionic-contacts	Calculates "ionic contacts" in the MD ensemble
mdutils-protein-contacts	Calculates protein contacts in the MD ensemble
mdutils-constava-wrapper	Infers residue-wise conformational states from the MD ensemble

Citation

The scripts in this repository were generated over the course of a large-scale simulation project. When citing this repository, please cite the associated publication:

Bickel, D. & Vranken, W. F. Effects of phosphorylation on protein backbone dynamics and conformational preferences. bioRxiv (2024) doi:10.1101/2024.02.15.580491.

License

This repository is licensed under MIT license.

Contact

- David Bickel - david.bickel@vub.be

- Wim Vranken - wim.vranken@vub.be