WARIO: Weighted fAmilies of contact maps to chaRacterize conformational ensembles of (highly-)flexIble prOteins

WARIO is a tool for the structural characterization of highly-flexible proteins. WARIO takes as input a conformational ensemble (e.g. generated form molecular dynamics simulations or other sampling methods) and represents it as a weighted family of contact maps. Contact is redefined by a continuous function, taking values in [0,1], that incorporates the relative orientation of the interacting residues as well as the sequence information. Then, the featured data is embedded into a 10-dimensional UMAP space and clustered using the HDBSCAN algorithm. Finally, the average values of the contact function across each cluster conformation are represented as cluster-specific contact maps. The maps are assigned with a weight given by the cluster occupancy.

Running WARIO

To run WARIO to characterize an ensemble, the user can directly execute the contact_clustering notebook, which contains the detailed pipeline and allows a step-by-step implementation of the tool.

Installing WARIO

WARIO and its required dependencies can be automatically installed if Python >=3.8 is available. We recommend to perform the installation inside a Python virtual environment. It can be created as follows

python3 -m venv pythonEnv
source pythonEnv/bin/activate

Then, WARIO is installed with

pip install -U pip
pip install git+https://gitlab.laas.fr/moma/WARIO.git

Once the installation is completed, the command

wario-notebooks

opens the ready-to-use jupyter notebook.

The installation procedure works correctly with recent versions of Linux (Ubuntu 20.04 and 22.04) and MacOS (Sonoma 14.4.1) operating systems. Typical install time on a normal desktop computer is around 5 minutes. If you encounter any trouble to install WARIO, please file an issue or contact us.