Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex

Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD
Journal of Chemical Theory and Computation 19:4863, 2023

We assess what is required for alchemical free energy calculations to be able to make high-quality predictions of the impact of interfacial mutations on protein-protein binding.

EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment

Wang Y, Pulido I, Takaba K, Kaminow B, Scheen J, Wang L, Chodera JD
preprint: [arXiv]

We present a drop-in replacement for generating AM1-BCC ELF10 charges based on graph convolutional nets that is orders of magnitude faster than standard methods for both small molecules and biomolecules.