Barcelona: probably the first city in the world to name a street after the CASP competition

Very sad to hear about the passing of Peer Bork, one of true giants of computational biology www.embl.org/news/embl-an...

In remembrance of Peer Bork  | EMBL

EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

embl.org

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...

Global comparative structural analysis of responses to protein phosphorylation - Nature Communications

Phosphorylation is central to protein regulation, yet its structural mechanisms remain poorly understood. Here, the authors conduct a global, systematic analysis of phosphorylated versus non-phosphory...

nature.com

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....

Protein interaction mapping reveals widespread targeting of development‐related host transcription factors by phytoplasma effectors

This work shows that the effectors of phytoplasma, a globally economically important bacterial plant pathogen, have pervasive interactions with development-related host transcription factors, providi...

onlinelibrary.wiley.com

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.

PMC Protein Modules Community@pmc-modularity.bsky.social · 2y ago

Join us for our new online seminar series, featuring two talks on protein modules every month! The first session kicks off at 6pm CET Feb 10 with Dr. Gergő Gógl and Dr. Ugo Dionne. Register to attend: tinyurl.com/register-pmc-seminar

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

The never-ending pandemic

Horizons - Issue 143

horizons-mag.ch

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

De novo designed proteins neutralize lethal snake venom toxins - Nature

Deep learning methods have been used to design proteins that can neutralize the effects of three-finger toxins found in snake venom, which could lead to the development of safer and more accessible an...

nature.com

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...

Modeling Bias Toward Binding Sites in PDB Structural Models

The protein data bank (PDB) is one of the richest databases in biology. The structural models deposited have provided insights into protein folds, relationships to evolution, energy functions of struc...

biorxiv.org

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

Allosteric Communication Mediated by Protein Contact Clusters: A Dynamical Model

Describing the puzzling phenomenon of long-range communication between distant protein sites, allostery is of paramount importance in biomolecular regulation and signal transduction. It is commonly as...

pubs.acs.org

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

Alán Aspuru-Guzik@aspuru.bsky.social · 2y ago

Post a PERFECT album from the 90’s that is neither Nirvana nor Pearl Jam.

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/...

PhD student - Machine learning in bio- and cheminformatics

wur.nl

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... .