Ollivier-Persistent-Ricci-Curvature

This repository includes the codes used in the work of Ollivier Persistent Ricci Curvature (OPRC) in Protein-Ligand Binding Affinity Predictions. This work has shown that OPRC delivers meaningful and interesting geometrical features in biomolecular data which is able to predict binding affinities with comparable performance to many existing traditional molecular descriptors and advanced mathematical based machine learning models.

It can also be seen that the geometrical information gathered from ORC also plays as an unique feature in differentiating osmolytes in hydrogen bonding networks.

Publications

• Wee, J., & Xia, K. (2020). Ollivier persistent Ricci curvature (OPRC) based molecular representation for drug design. arXiv preprint arXiv:2011.10281.
• JunJie Wee and Kelin Xia, "Ollivier persistent Ricci curvature (OPRC) based machine learning for protein-ligand binding affinity prediction", Journal of Chemical Information and Modeling, accepted (2021)

Cite

If you use this code in your research, please considering cite our paper:

@article{wee2021ollivier,
  title={Ollivier Persistent Ricci Curvature-Based Machine Learning for the Protein--Ligand Binding Affinity Prediction},
  author={Wee, JunJie and Xia, Kelin},
  journal={Journal of Chemical Information and Modeling},
  volume={61},
  number={4},
  pages={1617--1626},
  year={2021},
  publisher={ACS Publications}
}