I have developed a user-friendly tool to perform feature-based conformational clustering from MD simulations. It is a package containing several sub-commands and some of the commands are very similar to the GROMACS Analysis tools.
Following tutorials have been provided in the documentation:
- Protein clustering using PCA
- PCA-based ligand clustering
- Distances-based clustering
- Clustering of flexible Proteins using distance-matrix PCA
- Clustering of cavity/channel shapes
- Protein-Ligand Interaction Clustering
GitHub Repo: GitHub - rjdkmr/gmx_clusterByFeatures: Features Based Conformational Clustering of MD trajectories. See details at:
Documentation: https://gmx-clusterbyfeatures.readthedocs.io/
The manuscript is currently under preparation. Feedbacks and suggestions are welcome!