OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

Open position at the Swiss Institute of Bioinformatics: We are looking for a Director of the Center of Pathogen Bioinformatics apply.refline.ch/499599/0346/... I am in the Center's steering board together with fantastic colleagues (Emma Hodcroft @firefoxx66.bsky.social, Richard Neher @neher.io, and

Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications! www.nature.com/articles/s41...

Excited to share my PhD research, now on bioRxiv! We report a proteo-transcriptomic reprogramming and resource reallocation in the aging brain. Co–first author with Verena Kluever. Grateful to @forna.bsky.social‬ for mentorship, and to @tatjanat.bsky.social‬, Carlos López Otín & all collaborators🧠

Today in predatory journal spam: plagiarizing 15% of your manuscript is OK

Good to know our paper on the protein-protein interaction network between phytoplasma effectors and host proteins is getting attention: it's a #TopViewedArticle in TPJ @theplantjournal.bsky.social onlinelibrary.wiley.com/doi/full/10....

If anyone has any tips for fellowships or grants or giftfunds our group can apply for (in the US), please send our way. So far, we've not had much luck in raising funds... 💰 In this relatively popular area, so I feel like I'm doing something wrong 😅

A protein language model trained to predict subcellular localization for human proteins can generate de novo sequences with the desired localization and identify pathological mutations. @itamarchinn.bsky.social @pgmikhael.bsky.social www.science.org/doi/10.1126/...

At ALLOX @alloxbio.bsky.social in Barcelona we now have 3 computational positions available! 📌Structural Bioinformatics Scientist 👉 tinyurl.com/3rs46j4t 📌Platform Bioinformatician 👉 tinyurl.com/nyvazbke 📌Computational Chemist 👉 tinyurl.com/5n6vpem3 Apply or repost to help us spread the word 🙏

Looking forward to the monthly on-line seminars organized by the Protein Modules Community @pmc-modularity.bsky.social and talks on SLiMs, systems biology, signaling, computational biology and much more. First talks by Dr Gogl @teamgogl.bsky.social and Dr Dionne @gingraslab.bsky.social.

Long Covid: The never-ending pandemic in the magazine of @snsf-ch.bsky.social www.horizons-mag.ch/2024/12/02/t...

Deep learning methods aid in de novo design of proteins to neutralize lethal snake venom toxins in vitro and protect mice from a lethal neurotoxin challenge. www.nature.com/articles/s41... #NBThighlight

The Nobel Prize-winning chemist, Martin Karplus, has passed away. A pioneer in the theory and computation of the dynamics of macromolecules. 🧪 #ChemSky

Are PDB models biased in terms of how well they explain the underlying experimental data and are modeled? www.biorxiv.org/content/10.1...

#compchem Good read: Allosteric Communication Mediated by Protein Contact Clusters: A Dynamical Model #compchemsky pubs.acs.org/doi/10.1021/...

So many easy choices, but I'll go for this

How much of computational biology is doing detective work trying to figure out why some program won't run?

For those around Zurich, I'll be at the Zurich Seminar in #Bioinformatics this Thursday to talk about my work on the impact of phosphorylation on protein structure: compbiozurich.org/news/2024/20...

Here's a first: I'm hiring a PhD student. If you have (or know someone who has) a strong background and interest in computational (bio)chemistry or computer science (especially 3D computer vision), let's work together 😊 www.wur.nl/nl/vacature/...

Dear hivemind, in the absence of a fresh CAFA publication: what predictor(s) do people consider to be the state-of-the-art in protein function prediction nowadays? #bioinformatics #bioml #protein

Assessors’ conclusions of the 3D category (individual protein chains) of #CASP16 🧪

#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .