New Publication: Alchembed Philip Fowler, 12th June 2015 In much of my research I’ve looked at how proteins embedded in cell membranes behave. An important part in any simulation of a membrane protein is, obviously, putting it into a model membrane, often a square patch of several hundred lipid molecules. This is surprisingly difficult: although a slew of methods have been published, none of them can embed several proteins simultaneously into a complex (non-flat) arrangement of lipids. For example, a virus, as shown in our recent paper. Here we introduce a new method, dubbed Alchembed, that uses an alternative way, borrowed from free energy calculations, of “turning on” the van der Waals interactions between the protein and the rest of the system. We show how it can be used to embed five different proteins into a model vesicle on a standard workstation. If you want to try it out, there is a tutorial on GitHub. This assumes you have GROMACS is setup You can get the paper for free from here. 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 molecular dynamics publication research
research So…. I’m a Software Sustainability Fellow 19th December 2013 I’m pleased to announce that I am one of the Software Sustainability Fellows for 2014…. 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 preprint: Infection Inspection 12th December 202312th December 2023 Some great work by Conor Feehily, Nicole Stoesser and others, including collaborators from the Department… 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
publication New Publication: Proteins Alter the Stiffness of Membranes 23rd September 201629th September 2018 Although there have been many studies of proteins whose primary function is to ‘sculpt’ the… 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