Tassos Perrakis

7/11 onwards, the best bit ☺️

Read the whole thread by @daaninthelab.bsky.social : a power walk to a great adventure! Very proud of her and @rborza.bsky.social and the whole team!

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression Zinc finger proteins (ZNFs) are the largest family of transcription factors, yet how they activate gene expression remains unclear. In this study, we identified Zincore, a protein complex consisting o...

In today’s publication in Science we introduce Zincore: a novel protein of QRICH1 and SEPHS1 and functions as a transcriptional coregulator dedicated to zinc finger transcription factors. Here’s how we found it: 🧵 www.science.org/doi/10.1126/... 1/11

Type VI inhibitor targeting both the catalytic site and the tunnel of Autotaxin (ATX). PDB ID: 9FXW

🚨New Article Out!!

📢 In our latest work, we propose a Three-Point Lock binding mode for ATX inhibitors 🔒

🚀 This approach may represent the final piece in the puzzle of known binding mode types — and could have therapeutic relevance

♥️ Thanks for your support
Read more here: doi.org/10.1016/j.bm...

Dr. Ida de Vries!

#Tempi #Amsterdam

Very happy for my collaborator at the @embl.org Grenoble who led the microdiffractometer engineering project! Very well deserved prize.

This will go well.

An opinion piece by @wouterhm.bsky.social , featuring ideas from all authors which are beautifully illustrated by @rborza.bsky.social : Unlocking the signaling potential of GPI-anchored proteins through lipolytic cleavage www.cell.com/trends/cell-...

Postdoctoral Researcher in Structural Virology This project is focused on deciphering the role of virally encoded AAA+ ATPases in the replication cycles of Enteroviruses and Noroviruses.

I’m looking for a postdoc to join my team under a recently funded ERC Starting Grant.

If you’re passionate about structural #virology and have experience in #cryoEM SPA and/or #cryoET, get in touch!

Application deadline: January 19th.

Please share with your networks 🙏

Job link: tiny.cc/7v33001

Easy access to the AlphaFold 3 and PAE and PDE matrices with improved annotation (chain borders as vertical and horizontal lines) and to the #AlphaBridge PMC matrix.

Redesigned entry page with new logo from @rborza.bsky.social

🟥 Tutorial, F.A.Q., Credits and Contact details
🟧 Three examples to explore different features with protein-protein protein-DNA and protein-DNA interactions

New features in #AlphaBridge implemented by @alvarezsalmoral.bsky.social

🟥 Customisable cutoff-level for filtering on weak (0.5) or strong (0.9) interactions.
🟦 Displaying the ipTM score, and the brand-new "Contact-ipTM and #AlphaBridge scores.
🟧 Per-interface #AlphaBridge scores.

JBP1 and JBP3 have conserved structures but different affinity to base-J Base-J (β-D-glucopyranosyloxymethyluracil) is an unusual kinetoplastid-specific DNA modification, recognized by base-J containing DNA (J-DNA) binding …

Fast-forward: Ida de Vries revisited the old crystal structures, made new discoveries, and revived the project. Published today, this work may not change the world, but it reflects science's quieter side: missteps, small victories, and perseverance. Here's to the bittersweet journey of discovery.

During the COVID era when I was compulsively scrolling through the toxic wasteland of Tweeter I spotted this: A common contaminant? Turned out, we’d been analyzing a bacterial protein (same MW and DNA binding affinity) all along. Experimental science can be humbling, even crushing at times.

Few years ago, our collaborators on the "base J" project identified the JBP3 protein. We had determined the crystal structure of the DNA-binding domain, but we could never make sense of the cryo-EM reconstructions of full-length JBP3: nice single particles, but AlphaFold models did not fit the maps.

We need an @instruct-eric.bsky.social starter pack!

Thrilled to present Alphabridge in the Computational Chemistry session at #NWOChains! We aim to facilitate researchers to analyze interacting interfaces in predicted biomolecular structures. Honored to share insights with top chemists in the Netherlands. 🚀🔬 Preprint: www.biorxiv.org/content/10.1...

Greece got exactly 0 ERC consolidator grants this year.

0 grants to mid-career outstanding scientists for curiosity driven research at the highest level.

Maybe a statistical fluke?

Or a result of chronic national underfunding, insane bureaucracy, unfairness, opacity, nepotism, and low income?

Surely you have been using AlphaFold3 for your research project? If so, have you considered #AlphaBridge to analyze the output for macromolecule complexes prediction?

Web server: alpha-bridge.eu

Preprint: www.biorxiv.org/content/10.1...

New features coming soon!

📢 Applications for the NKI PhD program open from Jan 1 - Feb 28. Join our international research community in Amsterdam, working in cancer biology, AI research & life sciences with leading scientists and top facilities #PhD #CancerResearch More info: bit.ly/3O4bOjq

Today, a cancer patient advocate claimed that: ‘There is excellent research but not enough translation.’ While I appreciate the sentiment, I disagree profoundly. The issue isn’t just about translation—it’s that we don’t yet have enough excellent research to identify what will truly impact patients.

An excellent talk by @andreasbender.bsky.social on the real (and often overstated) impact of AI in drug discovery, offering balanced insights that cut through the hype, along with valuable ideas and suggestions for improvement.

Delaying and shortening the duration of treatment with CDK4/6 inhibitors in patients with metastatic breast cancer leads to similar survival outcomes while reducing toxicity and achieving substantial cost savings, the SONIA trial shows. Read more ➡️ bit.ly/3Oqw7aX

The Royal Academy of Sciences of the Netherlands (KNAW) today joined the protest against the unprecedented cuts on science and education. These cuts, threaten the prosperity, well-being and health of the country. As scientists, we all need to make our voices heard. Stop cutting back on science.

ARP/wARP had been rejected by Nature Structural (Molecular) Biology. I sent back a rebuttal, which, as I learned years later, was discussed over dinner with a famous colleague who told-off the editor for rejecting the paper. That paper remains the most cited in the journals’ history.

YouTube video by KNCV Eiwitten voor het volk - Tassos Perrakis

Proteins for the people!

A few words about what I do and why.

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