Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding

Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M Rangwala, Jessica B White, Joseph P Bluck, Jenke Scheen, William G Glass, Jiaye Guo, Sikander Hayat, Bert L de Groot, Andrea Volkamer, Clara D Christ, Markus A Seeliger, John D Chodera.
[bioRxiv]

We show that alchemical free energy calculations have the potential to prospectively predict the impact of clinical kinase mutations on targeted kinase inhibitor binding.

Nutmeg and SPICE: Models and data for biomolecular machine learning

Peter Eastman, Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland
Journal of Chemical Theory and Computation 20:8583, 2024.
[DOI] [preprint]

We present a significant expansion of the SPICE dataset, a large-scale quantum chemical dataset for training machine learning potentials, and show how it can be used to build extremely accurate machine learning potentials.