New preprint: Predicting antibiotic resistance in complex protein targets Philip Fowler, 4th January 20224th January 2022 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 binding free energies are, somewhat inevitably given the sizes of the DNA gyrase and RNA polymerase, large. Hence this work complements earlier work on a much smaller protein, DHFR, that demonstrated the method can be successful, but of course the predicted errors are much smaller — to the point that one can accelerate the computation by using large numbers of very short simulations. 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 group molecular dynamics publication research tuberculosis
antimicrobial resistance Updated preprint: predicting pyrazinamide resistance 21st November 20238th December 2023 This study was performed by Josh Carter back in 2019 and we uploaded a preprint… 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
computing GROMACS on AWS: Performance and Cost 17th January 20163rd March 2019 So we have created an Amazon Machine Image (AMI) with GROMACS installed. In this post… 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
computing GROMACS 4.6 18th October 201323rd September 2018 GROMACS is a scientific code designed to simulate the dynamics of small boxes of stuff, that… 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