STOP using ipTM for #AlphaFold PPI screens. * Artificially LOW when both full-length proteins have irrelevant, non-binding IDRs/domains. * If one protein is folded & other contains irrelevant IDRs or domains, the score is too HIGH bc of d0. * Use ipSAE or LIS. www.biorxiv.org/content/10.1...

Talks from #ColabW26 are now up on youtube! I was especially waiting for the recording of the talk by @malvikasharan.bsky.social This one is easily in my top-5 talks I ever attended. Moving, powerful and stimulating youtu.be/sjmRJQL8PoE?...

Have you ever wanted to try Snakemake workflows, but unsure where to start? Or maybe you use Snakemake, but want to interest your colleagues as well? Never heard of Snakemake? You are about to discover something exciting! Take a look at my quick-start tutorial github.com/Aleksandr-bi...

Oh no, I will have to remember 12 characters instead of 4 now…

This is so cool! Efficient sharing of molecular dynamics data is such a lacking element to empower FAIR practices in molecular simulation research

For today’s group meeting I gave a tutorial on workflows and Snakemake for molecular simulations 🙌🏻

With the #ColabW26 I discovered so many cool projects and resources, so I might as well collect some of them in this thread Starting with Air Quality Stripes airqualitystripes.info

Kicked off my first SSI Collaboration Workshop as an online participant today! So many stimulating discussions and much food for thought. Stellar job from the organisers. I feel so involved even being so remote in Oxford 🙌🏻 #CollabW26

Having heard updates on this project at many stages from @robbieclark.bsky.social I can say that this is an amazing work. Congratulations to everyone on the team and to Robbie 🎉

Our latest paper in which we use multiple force fields to recover various conformations of the ribose transporter from E. coli. The work of DPhil student Nikolai Juraschko and postdoc Florencia Klein Rocha pubs.acs.org/doi/full/10....

The find of the week for me is RustSASA. So fast and easy to use! I had to work around with `rust-python-sasa` instead of using `MDAnalysis`, because I work with coarse-grained systems in MARTINI. But even then, it gave me ~6x speed-up on my analysis🙌 github.com/maxall41/Rus...

Very exciting to talk at the OxBacNet meeting held at @dunnschool.bsky.social Summarising mine and @sykhalid.bsky.social collaboration with @augustsilale.bsky.social to investigate a new ExbBD motor structure using molecular dynamics (foreshadowing the manuscript in preparation)