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
molecular dynamics Installing GROMACS with MPI support on a Mac 5th December 2014 GROMACS is an optimised molecular dynamics code, primarily used for simulating the behaviour of proteins…. 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 GROMACS2018 on NVIDIA DGX-1s 27th September 201929th October 2019 HECBioSim advertised for proposals to use JADE, the new Tier-2 UK GPU high performance computer… 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 Is Software a Method? 1st April 201523rd September 2018 Last month I went to the Annual Meeting of the US Biophysical Society. As a… 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