New preprint: rapid prediction of AMR by free energy methods Philip Fowler, 15th January 202015th January 2020 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. Several of us were talking in the coffee break, I think about how the lambda simulations in the DHFR study are very short (250 ps), and I remember thinking “I wonder how short we could make them and still be able to qualitatively predict whether a mutation confers resistance or not?”. Turns out that answer is very, very short! But, you need to do a large number of repeats. The combined effect, however, is that, in principle, one can make a prediction (for DHFR at least) using about a tenth of the computational resource we originally used. Not only that, but since all the individual simulations are now only 50 ps long, one could theoretically run them all in parallel in less than ten minutes using GPUs. Overall, however, you would spend far longer creating the simulation input files (grompp in GROMACS), copying them onto the high performance computer, submitting them to the queue and retrieving and analysing the files! That is a problem for another day… 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 clinical microbiology computing GPUs molecular dynamics publication research
antimicrobial resistance BashTheBug Coordinator post advertised 15th November 2019 We are advertising for a Part-time Citizen Science Project Co-ordinator to come and work with… 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
New publication: detecting minor populations important for predicting fluoroquinolone resistance 5th April 20238th December 2023 When predicting if an infection is resistant or susceptible to a specific antibiotic, it is… 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
antimicrobial resistance New publication: Predicting resistance is (not) futile 21st August 201921st August 2019 Our “First Reactions” article has been published in ACS Central Science. We discuss the paper,… 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