RelaxDB Dataset

The RelaxDB and RelaxDB-CPMG datasets are curated data of relaxation-dispersion NMR data. This dataset was used to evaluate our model Dyna-1. Both the model and the datasets were introduced in our paper "Learning millisecond protein dynamics from what is missing in NMR spectra".

This HF datasets hosts the files for the RelaxDB data. More information on analysis from the paper, evaluation of the dataset using Dyna-1, or the Dyna-1 model itself can be found on GitHub.

Overview

RelaxDB: contains .json files describing the proteins for RelaxDB and RelaxDB-CPMG datasets and a .xlsx file with metadata of the curated proteins.

af2_pdbs: contains all of the af2 models used for input and evaluation in .pdb format

pkl_files: contains all of the .pkl files (one per protein) for RelaxDB and RelaxDB-CPMG datasets.

probs: contains saved frequencies from mBMRB-Train, stored for calculating dummy baselines.

split_files: contains split files for the provided datasets.

Citation

If you are using our code, datasets, or model, please use the following citation:

@article {Dyna-1,
    author = {Wayment-Steele, Hannah K. and El Nesr, Gina and Hettiarachchi, Ramith and Kariyawasam, Hasindu and Ovchinnikov, Sergey and Kern, Dorothee},
    title = {Learning millisecond protein dynamics from what is missing in NMR spectra},
    year = {2025},
    doi = {10.1101/2025.03.19.642801},
    journal = {bioRxiv}
}

Acknowledgements

We thank Katie Henzler-Wildman, Magnus Wolf-Watz, Elan Eisenmesser, J. Patrick Loria, Marcellus Ubbelink, George Lisi, Sam Butcher, and Nicolas Doucet for sharing data. We thank Martin Stone for sharing the Indiana Dynamics Database data his group curated in 2000.