In this paper, Alice Brankin calculates how different mutations in the DNA gyrase affect the binding of an antibiotic, moxifloxacin, and thereby potentially whether those mutations confer resistance or not. She calculates the relative binding free energy using thermodynamic integration, a method that is derived from classical statistical mechanics. To accompany these results, Philip Fowler, […]
Category: molecular dynamics
In this preprint, which Alice has been working on for several years, we show how alchemical free energy methods can predict whether an amino acid mutation confers resistance to an antitubercular, but only in cases where the change in binding free energy is large. This is mainly because the confidence limits on the change in […]
The idea for this paper arose during talking over coffee at the BioExcel Alchemical Free Energy workshop in May 2019. We’d previously shown that alchemical free energy methods could successfully predict which mutations in S. aureus DHFR confer resistance to trimethoprim (and crucially, which do not). That is all well and good, but to do […]
The story behind this preprint goes back to the workshop on free energy methods run by BioExcel in Göttingen in May 2019. I gave a talk, based in part on the work I’d previously published showing how alchemical free energy methods are able to predict which mutations in S. aureus DHFR confer resistance to trimethoprim.
HECBioSim advertised for proposals to use JADE, the new Tier-2 UK GPU high performance computer back in April 2019. JADE is built around NVIDIA DGX-1s, each of which contains 8 Tesla V100 GPUs. I’d previously run some alchemical free energy calculations on ARCHER, the Tier-1 UK academic supercomputer that has a conventional architecture, thanks to […]
Our “First Reactions” article has been published in ACS Central Science. We discuss the paper, Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches, by Matteo Aldeghi, Vytautas Gapsys and Bert de Groot, which is in the same issue of the journal. Aldeghi et al. apply a series of methods to try and predict the effect […]