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 […]
Last month I was invited to give a talk on using alchemical free energy methods to predict antimicrobial resistance at a workshop in Göttingen organised by the Max Planck Institute for Biophysical Chemistry on behalf of BioExcel. You can read more about the meeting, which I hope will become a biennial event, here.
Due to the rise of antibiotic resistance, it is increasingly important that your clinician knows which antibiotics will work (and which will not). Traditionally, this is done in hospital microbiology labs by growing a sample taken from the infection site, and then testing how a range of antibiotics affect its growth, or, ideally, kill it. […]
DOCKER is cool. But what is it? From the DOCKER webpage Docker containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries – anything you can install on a server. This guarantees that it will always run the same, regardless of […]
Recently I’ve moved to the John Radcliffe hospital and my old lab kindly let me have some old servers that were switched off. This pushed me to learn how to setup them up as a compute cluster with a scheduler for running GROMACS jobs. I’ve wanted to learn this for years, having used many clusters […]
This is a Gramble, which of course is short for a GROMACS Bramble, or, in other words, a Raspberry Pi 2 model B cluster running GROMACS. Given the ARM processor in a Raspberry Pi 2 does not allow SIMD instructions like the more complex (and expensive) Intel chips, why would I want to do such […]