About MDANCE
Molecular Dynamics Analysis with N-ary Clustering Ensembles (MDANCE) is a flexible n-ary clustering package that provides a set of tools for clustering Molecular Dynamics trajectories. The package is designed to be modular and extensible, allowing for the addition of new clustering algorithms and similarity metrics. Research contained in this package was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R35GM150620.
Background
Clustering Algorithms
NANI
k-Means N-Ary Natural Initiation (NANI) is an algorithm for selecting initial centroids for k-Means clustering. NANI is an extension of the k-Means++ algorithm. NANI stratifies the data to high density region and perform diversity selection on top of the it to select the initial centroids. This is a deterministic algorithm that will always select the same initial centroids for the same dataset and improve on k-means++ by reducing the number of iterations required to converge and improve the clustering quality.
For more information on the NANI algorithm, please refer to the NANI paper.
eQual
eQual is a O*(N)* clustering algorithm that use the radial threshold to grow the cluster to maximize similarity between members in a cluster. It is an extension of the Radial Threshold Clustering algorithm [(Daura and Oscar Conchillo-Solé)](https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.2c01079). eQual has improved with new seed selection methods and tie-breaking criteria.
Clustering Postprocessing
PRIME
🪄 Predict Protein Structure with Precision 🪄
Protein Retrieval via Integrative Molecular Ensembles (PRIME) is a novel algorithm that predicts the native structure of a protein from simulation or clustering data. These methods perfectly mapped all the structural motifs in the studied systems and required unprecedented linear scaling.
For more information on the PRIME algorithm, please refer to the PRIME paper.
Contributing
Contributions to MDANCE are welcome!
License
MDANCE is released under the MIT License. See the LICENSE file in the project repository for more details.
Citing MDANCE
If you use MDANCE in your research, please cite the following paper:
@article{chen_k-means_2024,
title = {k-Means NANI: An Improved Clustering Algorithm for Molecular Dynamics Simulations},
issn = {1549-9618},
url = {https://doi.org/10.1021/acs.jctc.4c00308},
doi = {10.1021/acs.jctc.4c00308},
journal = {Journal of Chemical Theory and Computation},
author = {Chen, Lexin and Roe, Daniel R. and Kochert, Matthew and Simmerling, Carlos and Miranda-Quintana, Ramón Alain},
month = jun,
year = {2024},
note = {Publisher: American Chemical Society},
}
Contact
For questions or support, please contact us.