Understanding Ring Puckering in Small Molecules and Cyclic Peptides

This repository contains two python scripts (Ring_Analysis.py and Ring_Reconstruction.py) for ring conformational analysis and ring reconstruction respectively, see Example.ipynb for illustration. The data and molecule file contain precomputed puckering parameters and low energy ring conformations generated by our proposed sampling method. The results presented in ChemRxiv (https://chemrxiv.org/articles/preprint/Understanding_Ring_Puckering_in_Small_Molecules_and_Cyclic_Peptides/12999938) can be found in Ring Analysis, Cyclic Peptide Analysis, and Sampling Performance notebook.

Dependencies

• Numpy
• Pandas
• Matplotlib
• RDKit
• py_rdl (RingDecomposerLib) (https://github.com/rareylab/RingDecomposerLib)