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

Welcome to WARIO, an ensemble characterization tool. WARIO represents an ensemble 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 and MacOS operating systems. If you encounter any trouble to install WARIO, please file an issue or contact us.