@jurgjn.bsky.social
Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
22.07.2025 14:13 — 👍 85 🔁 30 💬 3 📌 3
The war on science in the US is already having an effect on private sector research like AlphaFold. Bears repeating but the private sector builds on top of things created by academic research for the public good. This hurts everyone.
28.05.2025 10:18 — 👍 240 🔁 106 💬 2 📌 12
Examples of alternate conformations with environmental explanations. (A) a protein in two states (open and closed) mediated by allosteric effects; (B) a population of two discrete rotamer states of a sidechain; (C) bound and unbound states due to ligand interaction; (D) different oxidation states of a cysteine pair. Furthermore, some regions in many protein structures exhibit such a degree of flexibility, that no accurate modelling is possible (dashed lines, E). The backbone conformation cannot be determined with crystallographic methods in such cases.
Failure of ensemble prediction algorithms in altloc segments. Although structure and ensemble prediction techniques based on amino acid sequences are capable of accurately reconstructing the overall backbone structure (left column), they consistently fail to produce viable samples corresponding to one of the two altloc conformations (as shown in the magnified regions in the second through fourth columns).
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...
I miss when the biggest controversy about mRNA was whether it correlated with protein or not.
20.03.2025 13:31 — 👍 319 🔁 40 💬 10 📌 3LLMs can't take responsibility for their mistakes. When a human journalist puts their name on AI-written text, they take on that responsibility.
Increasingly I see inaccurate and badly written news stories authored by AI, many of which have actual humans listed as authors or editors.
The best first sentence of a grant application I've read was (paraphrasing), "Tool X is widely used to do task Y; we will make it accessible to people living with condition Z (13% of the population) so that it is more equitable and more widely used". Let's unpack why, because there's a lesson. 🧵
05.12.2024 22:13 — 👍 225 🔁 40 💬 25 📌 5
We’ve now explored this on all GPU models available on our cluster and some non-A100/H100 do not have the issue; seems like something nuanced that can hopefully be fixed:
github.com/google-deepm...
We’ve now explored this on all GPU models available on our cluster and some non-A100/H100 do not have the issue; seems like something nuanced that can hopefully be fixed:
github.com/google-deepm...
Jurgen in our group run AF3 locally after fiddling. It worked well on a A100 and produced some bad models on a lower end GPU. We don't have access to many A100s so unless we get it working on lower-end GPUs we won't be able to use this much.
14.11.2024 19:05 — 👍 17 🔁 2 💬 2 📌 0The former finished without errors, but the output was noise (something similar to 100% spaghetti with AlphaFold2). The latter finished with the structure posted by @pedrobeltrao.bsky.social (2/2)
15.11.2024 08:16 — 👍 1 🔁 0 💬 2 📌 0We tried running the example from README.md (“2PV7”) on a lower-end GPU with --flash_attention_implementation=xla (described in performance.md), and on an A100 GPU without that option. (1/2)
15.11.2024 08:16 — 👍 2 🔁 0 💬 1 📌 0
1. I'm conflicted about moving old tweets to Bluesky. I like the idea in general of using @blueark.app to preserve that content.
I have a few threads posted during COVID—for example, the original analysis of the IHME model right after it came out—that seem a valuable part of the scientific record.
