Miguel Correa

I appreciate this new season of Silicon Valley except for the part where we all live inside it.

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.

Very sad to hear about the passing of Peer Bork, one of true giants of computational biology

www.embl.org/news/embl-an...

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👇

Elastic analysis bridges structure and dynamics of an AAA+ molecular motor Author summary Molecular motors are proteins that transform chemical energy into motion. To do so, they change their shape through a highly organised cycle. How exactly these changes in shape translat...

And hey, while you’re here, take a peek at our collaborator's also just published paper on molecular motors, mixing biophysics and structural bioinformatics in a cool way.
🧬 journals.plos.org/ploscompbiol...

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

Thanks... and check your DMs! :)

And finally, our dataset is publicly available for anyone to explore or build on!

In collaboration with the Sartori Lab at the Gulbenkian Institute, we probed for mechanical coupling and found a small but significant subset of phosphosites mechanically linked to known functional sites. This kind of “mechanical relay,” however, appears to be the exception rather than the rule.

There can be dramatic changes in residue-residue couplings upon phosphorylation, an uncommon mechanism that has gone largely unnoticed in prior research.

Phosphorylation is frequently linked to local changes in thermal fluctuations, but rarely alters dynamics globally, pointing to an important role for entropic allostery.

The “phosphorylated conformations” we observe are already present among non-phosphorylated family members. In other words, phosphorylation selects from pre-existing states rather than "creating" new ones.

Phosphorylation generally causes small conformational changes, and phosphorylated structures tend to be more uniform than non-phosphorylated ones. Interestingly, the extent of structural change depends on both the phosphorylated residue and the predicted functionality of the phosphosite.

Surprisingly, those have been much less explored than you might think. So we asked: across the entire Protein Data Bank, how does phosphorylation affect protein structure? Here are some of the key highlights.

Protein phosphorylation is a key regulator of cellular processes: it’s everywhere, but the function and relevance of most phosphosites remain unknown. Understanding what these sites actually do means uncovering the structural mechanisms through which phosphorylation acts.

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...

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🧠

Protein Large Language Models: A Comprehensive Survey Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surve...

Protein LLMs are very much a thing. Instead of predicting missing words, they predict e.g. aminoacids in the protein sequence.
arxiv.org/abs/2502.17504

"You mean many more tools will start adding support for mmCIF, right? ...Right?"

Screenshot from predatory journal invitation spam: "To maintain the integrity of our journal, we would like to emphasise the importance of producing original and results- oriented articles with a maximum of 15% plagiarism, including references. We kindly request that you adhere to the scope of our journal and ensure that your hard work is protected."

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

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...

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 😅

Es el sketch del ascensor con reconocimiento de voz en Escocia de hace más de una década hecho realidad www.youtube.com/watch?v=HbDn...

ProtGPS classifies protein compartment with high performance.

Generative modeling creates novel proteins that concentrate in a desired condensate.

Pathogenic mutations are predicted to alter protein compartmentalization

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/...

Looks nice! As you mention, someone tried to do this with NMA before. Of course I expect to get better results with the correlation matrix from MD, but since it's orders of magnitude faster to run NMA than MD, wouldn't that be a better baseline to compare against?

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.

Siempre nos quedará Lisboa.

The never-ending pandemic Horizons - Issue 143

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

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...

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

YouTube video by Darude Darude - Sandstorm

The unofficial Finnish anthem?
www.youtube.com/watch?v=y612...