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Ben Hall

@hallben.bsky.social

Professor in computational cancer biology at UCL interested in disease, mutations, and aging. Funded by CRUK, MRC and Royal Society. Personal account for science, code, music, photography! “Tired is the new awake”

2,668 Followers  |  3,360 Following  |  887 Posts  |  Joined: 10.10.2023  |  1.9981

Latest posts by hallben.bsky.social on Bluesky

AI tools are immensely powerful. The use of AI as a general purpose chat bot that is used like an encyclopaedia is the worst possible use of AI. AI is now, given good instructions from a knowledgeable user, capable of doing absolutely vast amounts of work extremely fast.

29.01.2026 09:09 — 👍 249    🔁 45    💬 13    📌 20
Binding Entropy Can Be Predicted by Crystallographic Ensembles Protein-ligand binding is governed by free energy, comprising both enthalpic and entropic contributions. Yet structural interpretations of binding thermodynamics have predominantly focused on enthalpic interactions, largely neglecting entropy because it is difficult to quantify from static structural models. Here, we developed multiconformer ensemble models to analyze high-resolution X-ray crystallography structures and estimate both protein and solvent conformational entropies. These ensemble models successfully predicted experimental binding entropies measured by isothermal titration calorimetry for over 70 protein-ligand pairs across 12 proteins, revealing a strong linear correlation. Protein entropy, estimated using crystallographic order parameters that capture both harmonic and anharmonic motion, correlates linearly with experimental binding entropy. Incorporating resolution-corrected differences in water-molecule counts substantially improves predictions, demonstrating that protein and solvent contributions must be considered jointly. Analysis of water-protein hydrogen bonding networks partially explains entropic differences across complexes. These results establish that crystallographic ensembles can quantify binding entropy, enabling explicit entropic considerations in structure-based studies of molecular recognition for both functional analysis and drug design. ### Competing Interest Statement The authors have declared no competing interest. American Cancer Society, https://ror.org/02e463172

Miller & Wankowicz (2026) Binding Entropy Can Be Predicted by Crystallographic Ensembles. #bioRxiv #preprint #CompChem #PhysChem #biophys #cheminformatics #chemsky 🧪
doi.org/10.64898/202...

29.01.2026 10:35 — 👍 1    🔁 1    💬 0    📌 0

I think this is relatively common, although there’s some assessment on application

24.01.2026 09:35 — 👍 0    🔁 0    💬 0    📌 0
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UKRI pauses several funding calls amid priorities shake-up - Research Professional News “Period of transition” at funding agency sees some Medical Research Council funding opportunities on hiatus

This is all I could find

www.researchprofessionalnews.com/rr-news-uk-r....

23.01.2026 15:55 — 👍 0    🔁 0    💬 1    📌 0

👀

23.01.2026 15:53 — 👍 0    🔁 0    💬 1    📌 0

There’s been quite a lot of nothing good recently tbf

23.01.2026 12:47 — 👍 0    🔁 0    💬 1    📌 0

What’s happening?

23.01.2026 12:45 — 👍 0    🔁 0    💬 1    📌 0
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Airport Book Brain How faddish ideas keep seducing.

oh, this is really good on what @joxley.jmoxley.co.uk calls "airport book brain", where glib "solutions" are jumped on by politicians who want smooth narratives, discarding nuance and complexity. Complete with a nice pop at Jonathan Haidt, and at the "UPF" brigade, too. (ht @rorycj.bsky.social)

23.01.2026 09:55 — 👍 21    🔁 6    💬 4    📌 2

Oh! Is that just for one room, or multiple?

Been considering it for one or two rooms, but I believed you needed permission if it served more than one room.

22.01.2026 16:23 — 👍 0    🔁 0    💬 1    📌 0

What was the rule change?

22.01.2026 15:33 — 👍 0    🔁 0    💬 1    📌 0

Finally, the evidence I needed to show my kids that, "Yes, you did this to me!"

22.01.2026 05:54 — 👍 27    🔁 5    💬 1    📌 0
Simon van gelder played by Morgan Woodward. He looks older than 43, I tell myself

Simon van gelder played by Morgan Woodward. He looks older than 43, I tell myself

43 in Star Trek episode dagger of the mind

21.01.2026 22:33 — 👍 1    🔁 0    💬 0    📌 0

Honestly sometimes it’s like meeting a dog that talks total nonsense but in perfect English. It’s super impressive that it can do it at all, but it’s really not useful or helpful

21.01.2026 16:48 — 👍 1    🔁 0    💬 0    📌 0

Second preprint of the year in which @sarahgersing.bsky.social from @rhp-lab.bsky.social mapped the effects of >7500 variants in glucokinase (GCK) on the interaction with the glucokinase regulatory protein so that we now have a 3D GCK scan (abundance, interaction, activity)

doi.org/10.64898/202...

18.01.2026 18:14 — 👍 23    🔁 6    💬 0    📌 0

“Tell me you were trained on a bunch of stack overflow RTFM comments without telling me you were trained on stack overflow”

17.01.2026 12:11 — 👍 1    🔁 0    💬 0    📌 0

I did have some entertaining failures though. A particular high point was an increasingly aggressive set of repeated responses from chatgpt when its solution to a bug was incorrect

17.01.2026 12:09 — 👍 1    🔁 0    💬 1    📌 0

My deep suspicion is that what it’s doing is taking existing known solutions (and code) and fitting them to my spec- that is, it’s not inventive, it’s adapting in the way I would have to do from examples, stack overflow etc

17.01.2026 12:02 — 👍 0    🔁 0    💬 1    📌 0

The caveat is that I know exactly what I want and can describe and test the high level specifications from whatever is generated. I think it would have failed if I didn’t have a clear view, or if I couldn’t fix the issues manually myself.

17.01.2026 12:01 — 👍 1    🔁 0    💬 1    📌 0

My experience in the last 6 months has been
- the code is much more easy to read and works well enough for me to debug functionality to get it there
- for ugly to use functions (matplotlib) it’s really helpful in finding the combination of options I want
- its good at helping with cryptic errors

17.01.2026 11:59 — 👍 1    🔁 0    💬 1    📌 0
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a cartoon character is pointing at a chart that says disco record sales Alt: a cartoon character is pointing at a chart that says disco record sales, with unrealistic exponential growth

I’ve had some eye opening experiences with coding assisted by LLMs recently, and I wonder if at least some of the froth is down to the genuine success for programmers as consumers, and then incorrectly extrapolating to the rest of the world

17.01.2026 11:52 — 👍 3    🔁 0    💬 1    📌 0

I don’t think that’s fair. He wasn’t deeply technical but he had a unique understanding of both worlds.

If it was just marketing that determined his success at Apple, that level of success would be commonplace

17.01.2026 11:45 — 👍 2    🔁 0    💬 1    📌 0

Funny, but also one of the two best career pieces of advice I got -- get exercise, especially when you are too stressed or don't have time for it.

17.01.2026 06:21 — 👍 67    🔁 12    💬 3    📌 2

It’s not lost on me that it’s spending tokens like a sailor when it does this

16.01.2026 21:01 — 👍 2    🔁 0    💬 1    📌 0

I’ve found Claude has a propensity to be verbose, including going back to additionally and unnecessarily integrate new requests into older things that don’t need it

16.01.2026 20:16 — 👍 1    🔁 0    💬 1    📌 0

“Breakfast. Cups.”

16.01.2026 17:02 — 👍 0    🔁 0    💬 0    📌 0
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Artificial intelligence tools expand scientists’ impact but contract science’s focus - Nature Artificial intelligence boosts individual scientists’ output, citations and career progression, but collectively narrows research diversity and reduces collaboration, concentrating work in data-rich a...

One of my concerns with AI-assisted research in biology is that we're already looking only in the lamplight and AI incentivizes us to narrow the beam. Seems like it's happening...
www.nature.com/articles/s41...

15.01.2026 16:08 — 👍 148    🔁 43    💬 7    📌 7

I prefer this explanation to it being nostalgic for my favourite trackballs!

15.01.2026 11:55 — 👍 4    🔁 0    💬 2    📌 0

I don’t know/understand Logitechs business reasons, but I bought some switches this Xmas to revive my favourite of their trackballs, no longer for sale. Amazed how attached I (and others) to what are essentially cheap peripherals

15.01.2026 11:30 — 👍 2    🔁 0    💬 1    📌 0

'Another Warrington has hit the North-West'.

14.01.2026 13:18 — 👍 299    🔁 50    💬 54    📌 5

I’ve reposted this twice now, it’s great, and it’s getting referenced in my updated lecture covering the subject (alongside the 1979 IBM slide)

14.01.2026 10:10 — 👍 2    🔁 0    💬 0    📌 0

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