Lightnews — Scholar-powered news

Gina El Nesr @ginaelnesr.bsky.social · 27d

MLSB is coming to Copenhagen, DK 🎉

Submission is under the same portal, just simply indicate your location preference(s).

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 27d

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉

Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

1 2 3

Gina El Nesr @ginaelnesr.bsky.social · Aug 26

Diego del Alamo @delalamo.xyz · Aug 25

Can't find the words so heres a diagram, apologies for bad handwriting. Higher energy states that are in between the two conformations you care about are both more combinatorially plentiful, and rarer, and only a few of them matter. mAb CDRs can interconvert on 10s of µs so it matters for those too

1

Reposted by Gina El Nesr

Diego del Alamo @delalamo.xyz · Aug 21

... each independent simulation is 500 ns long, almost certainly too short to sample the sorts of large-scale functionally relevant conformational changes that ML methods should be learning from, which means I must once again repost this excerpt from Janson et al

2 1 9

Reposted by Gina El Nesr

Will Ratcliff @wcratcliff.bsky.social · Aug 12

Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.

21 130 360

Reposted by Gina El Nesr

Martin Pacesa @martinpacesa.bsky.social · Jul 25

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

23 39 220

Gina El Nesr @ginaelnesr.bsky.social · Jul 28

Uncancelled! 🥳

1 1

Gina El Nesr @ginaelnesr.bsky.social · Jul 28

The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬

Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟

1 2 11

Gina El Nesr @ginaelnesr.bsky.social · Jul 13

is this how small molecules bind?? 😼

1 1 5

Gina El Nesr @ginaelnesr.bsky.social · Jul 13

molecular cat-formations

1 1 4

Gina El Nesr @ginaelnesr.bsky.social · Jul 8

Enzyme design! Benchmark data! Wet-lab validation! Expression & activity assays!! ✨

The Align Foundation @alignbio.bsky.social · Jul 8

1/4
🚀 Announcing the 2025 Protein Engineering Tournament.

This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️

#AIforBiology #ClimateTech #ProteinEngineering #OpenScience

1 7

Reposted by Gina El Nesr

The Align Foundation @alignbio.bsky.social · Jul 8

1/4
🚀 Announcing the 2025 Protein Engineering Tournament.

This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️

#AIforBiology #ClimateTech #ProteinEngineering #OpenScience

1 20 23

Gina El Nesr @ginaelnesr.bsky.social · Jul 7

Seems it has happened in the past. Some examples are MLCB and MHLC, which were once conference workshops and after being rejected, they spun out into separate conferences.

1

Gina El Nesr @ginaelnesr.bsky.social · Jul 7

ugh we thought so too 😪 currently looking into alternative solutions!

1

Reposted by Gina El Nesr

Noelia Ferruz @noeliaferruz.bsky.social · Jul 7

Noooo😭
This was the BEST workshop at NeurIPS!!

Gina El Nesr @ginaelnesr.bsky.social · Jul 7

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.

Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”

More on the future of MLSB soon…

1 2 4

Reposted by Gina El Nesr

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Jul 7

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco

8 70 150

Gina El Nesr @ginaelnesr.bsky.social · Jul 7

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.

Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”

More on the future of MLSB soon…

2 5 8

Reposted by Gina El Nesr

Alexey Amunts @amunts.bsky.social · Jul 4

Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

www.science.org

45 63

Reposted by Gina El Nesr

Science Magazine @science.org · Jul 2

Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

scim.ag

4 33 81

Reposted by Gina El Nesr

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jul 2

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant
doi.org/10.1073/pnas...

[Following: Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon doi.org/10.1038/s414...

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant | PNAS

The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capi...

doi.org

4 12 37

Gina El Nesr @ginaelnesr.bsky.social · Jun 28

philosophy at its finest

7

Gina El Nesr @ginaelnesr.bsky.social · Jun 23

Oh well in that case, I guess this sequence is purification ready, with an SA spacer nicely placed for a TEV-tag insertion

2

Gina El Nesr @ginaelnesr.bsky.social · Jun 23

Ran some sequence design with LigandMPNN and it... designed a protein with an (almost) His-tag 🤔

1 4

Gina El Nesr @ginaelnesr.bsky.social · May 12

someone said we need a meme

1 6 27

Reposted by Gina El Nesr

Diego del Alamo @delalamo.xyz · Apr 27

"De novo prediction of protein structural dynamics"

I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...

delalamo.xyz

5 17 70