New publication: how quickly can be calculate the effect of a mutation on an antibiotic? Philip Fowler, 20th November 202020th November 2020 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 this at scale, we’d need to be able to run such calculations quickly, hence this paper. Part of the answer is making use of high performance computing, but part is also accepting that the primary goal of the calculations is not quantitative accuracy and precision, but instead resolving which side of a free threshold the change in antibiotic binding free energy induced by the mutation lies. That in turn enables the use of large numbers of very short lambda simulations which can be run in parallel, reducing the time-to-solution even further. This, or similar methods, could be used in drug development (to assess how many codon mutations could allow a protein to escape the action of an inhibitor) or in diagnostics. The paper is part of a special issue on Computational Medicine. Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance computing distributed computing GPUs molecular dynamics publication research
antimicrobial resistance New preprint: rapid prediction of AMR by free energy methods 15th January 202015th January 2020 The story behind this preprint goes back to the workshop on free energy methods run… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
distributed computing GROMACS in DOCKER: First Steps 23rd May 2016 DOCKER is cool. But what is it? From the DOCKER webpage Docker containers wrap up… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
clinical microbiology New publication: Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers 13th January 202113th January 2021 A second Covid-19 publication I’m proud to be (a small) part of has recently published… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More