delalamo.xyz - Profile | ThreadSky | a Reddit-style client for Bluesky

Long shot but does anyone have code examples for how to embed an MD simulation into a web page? For example on this page, on '3D viewer' -> dynamics: www.dsimb.inserm.fr/ATLAS/databa... 🧶🧬

submitted 12 hours ago • 4 comments

TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...

submitted 3 days ago • 1 comment

A PLM's ability to accurately predict variant effects (e.g., whether mutations are beneficial or deleterious) can be inferred from the perplexity of its prediction, regardless of scale www.biorxiv.org/content/10.1...

submitted 2 days ago • 0 comments

Super excited to share a new preprint from our lab on design of small-molecule binding proteins using neural networks! The paper has a bit of everything. A new graph neural network, new design algorithms, and experimental validation. www.biorxiv.org/content/10.1... 🧵🧪

submitted 4 days ago • 2 comments

Really nice resource from @delalamo.xyz !! Wanna mention the "AdK test" we're noticing newer DL methods fall short on: many proteins (like AdK) that have apo/holo conf change sample both the apo/holo state even without ligand bound. But w/o ligand bound, they are mainly in the apo state

submitted 4 days ago • 1 comment

"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_...

submitted 5 days ago • 5 comments

Encode protein structures as a series of discrete tokens, train a language model, and sample protein structural conformations given the sequence. arxiv.org/abs/2410.18403

submitted 6 days ago • 2 comments

Hey @kmichie.bsky.social any chance you can remove alphafold as a keyword from the protein cosmos feed? It's bringing in quite a bit of junk

submitted 5 days ago • 3 comments

Choosing ML architectures for protein engineering is often challenging. Our “new” updated preprint provides a rational framework to match ML models to protein fitness tasks, showing landscape ruggedness influences prediction accuracy. Mahakaran dana Adam et al www.biorxiv.org/content/10.1...

submitted 10 days ago • 0 comments

Close to recreating it in ChimeraX: 1. Install the python file: github.com/smsaladi/chi... 2. rainbow palette magma 3. col modify #1 blackness - 40 4. col modify #1 whiteness - 40 5. col modify #1 saturation - 50 6. col modify #1 lightness + 20 Room for improvement, needs more desaturation

submitted 16 days ago • 3 comments

This structure is absolutely _nuts_. Lipids are captured marching through the tunnel

submitted 6 days ago • 1 comment

There are now a trio of great pieces covering the rapid rise of Chinese biotech: - atelfo.github.io/2024/12/20/w... - centuryofbio.com/p/commoditiz... - www.asimov.press/p/china-trials

submitted 8 days ago • 4 comments

An interesting "what have we been doing all these years?" result from this paper is how sub-optimal the widely-used uniform sampling scheme can be (cluster all @50%, sample from all clusters equally). In contrast, strategies that account for the relative differences in cluster size improve val loss

submitted 8 days ago • 1 comment

Some crystal structures show evidence of multiple stable conformations, such as loops or side chains with two distinct regions of density. These can be correctly modeled by MD, but not modern protein ensemble prediction tools like AlphaFlow or DiG (BioEmu not tested) www.biorxiv.org/content/10.1...

submitted 9 days ago • 0 comments

TIL that Claude Code increases the "thinking" budget to maximum if you tell it to "ultrathink", which is a step up from "megathink", which is a step up from "think" simonwillison.net/2025/Apr/19/...

submitted 12 days ago • 9 comments

It's a shame this account stopped posting because it's asking many of the same questions I have

submitted 10 days ago • 0 comments

Brings back fond memories of my PhD supervisor complaining about all the money I was wasting on biobeads during nanodisc and proteoliposome reconstitution

submitted 11 days ago • 0 comments

ProGen3 is out and shows a cool result: as PLMs get larger, they can successfully generate across a broader cross-section of the protein fold space www.profluent.bio/showcase/pro...

submitted 11 days ago • 1 comment

"If you're used to being able to sit down and bang out code, any time, anywhere, with all kinds of tools (libraries, compilers, virtual machines, what have you) at your fingertips, then yeah, working up a new assay protocol in a cell line is going to seem agonizingly slow" (from 2015)

submitted 11 days ago • 0 comments

PLMs fine-tuned on protein structural dynamics data show improved zero-shot variant effect prediction. However, this improvement is lost as the number of homologs in the training set increases. The data for fine-tuning includes MD and NMA data www.biorxiv.org/content/10.1...

submitted 11 days ago • 1 comment

I'm moving back to Cambridge MA USA in two months and all signs point to some real scouring-of-the-shire vibes waiting for me

submitted 17 days ago • 0 comments

Q: anyone have a GIF or video of one of these DE Shaw millisecond MD simulations? It’s for a PPT so needs to be small-ish

submitted 19 days ago • 0 comments

LogMD is such an awesome package I only just now became aware of. Here's an example of someone using it to show RFDiffusion trajectories (which are still fun to look at despite not being mechanistically insightful)

submitted 19 days ago • 0 comments

Structural basis for the substrate recognition and transport mechanism of the human y+LAT1-4F2hc transporter complex. @ScienceAdvances Check this #membrane #protein in the UniTmp database: https://pdbtm.unitmp.org/entry/9kh5

submitted 21 days ago • 0 comments

Unfortunately no github repo for RFDiffusion2!

submitted 21 days ago • 2 comments

Atom level enzyme active site scaffolding using RFdiffusion2 [new] Enables enzyme design from sequence-agnostic functional group locations, solving prior limitations of residue-level constraints and fixed catalytic residue positions.

submitted 21 days ago • 0 comments

This was fun! Thanks for tuning in and if you didn't catch it live, you can still listen on demand via the same link. We recently published the work on bioRxiv (final version soon in eLife): www.biorxiv.org/content/10.1... And the sequenced RSV antibody: www.biorxiv.org/content/10.1...

submitted 22 days ago • 0 comments

AlphaFold3 more or less universally predicts the active state of ligand-bound GPCRs, even in cases where the ligand is an antagonist that stabilizes the inactive state www.biorxiv.org/content/bior...

submitted 22 days ago • 0 comments

This has been a long journey, but it's now out in final form. @kjamali.bsky.social academic.oup.com/bioinformati...

submitted 24 days ago • 0 comments

Distantly related proteins w/ the same fold can respond differently to ligand binding, even when the ligand-binding site is unchanged www.biorxiv.org/content/10.1...

submitted 24 days ago • 1 comment