Dr. Ida de Vries!

#Tempi #Amsterdam

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-...

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.

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.

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!

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.

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.