Daniel Alvarez

👨🏻‍💻Drug Discovery | Compchem | Software Engineer | method development #mdmix | 👨🏼‍🎨🎨Oil painting

[Daniel Alvarez @daninthenet]

@MrBitcoinWhalee @grok @NoLimitGains Yeah sure

[Daniel Alvarez @daninthenet]

@Barbijaputa @srtaVanDerHelst @Domestika me ha renovado sin saberlo y yo consentirlo. Pago de 300€!!!! de anualidad de algo que no uso. Buscando encontré todo este tema. Al final conseguisteis algo?

[Daniel Alvarez @daninthenet]

@Domestika me renovaron automáticamente una suscripción que no quiero ni utilizo. La cuota además subió muchísimo a 300€. Era totalmente inconsciente de esto. Quiero devolverla y que un reembolso. Es un trato abusivo por mucho que esté en los términos y en las web.

[Daniel Alvarez @daninthenet]

Wait! So the “peer” in peer-reviewing… is now an AI agent?

[nature @Nature]

Researchers have been sneaking secret messages into their papers in an effort to trick AI tools into giving them a positive peer-review report

Read the full story: https://t.co/1kOYRLf72i

[Gabriele Corso @GabriCorso]

📢 Call for proposals: Boltz small-molecule design collaboration! 🧬
Can we help design your ideal molecule? Can you help us improve our open-source models? Please reach out or share with scientists you know! More details below!

It has been great to see the level of excitement around our Boltz-2 release. Along with the structure and affinity model, we are working on new workflows for hit-discovery and hit-to-lead of small molecules. We have seen very strong computational results and we are now interested in validating them across a range of different targets and real-world settings.

Do you have a target on which you would like to design or optimize small-molecule binders? Do you have an associated chemical or functional assay that you can run to validate the designs? If the answer is yes to both questions, we would love to hear from you and collaborate.

As part of these collaborations, we would work alongside you to tailor our workflows for your task, run the large scale design on our cluster, and return to you the designed molecules alongside their expected scores. We ask you to commit to testing the top (according to your judgement) designed compounds and send us back the experimental results within 2 months of the selection.

You’ll have full IP of the compounds we send you and have the opportunity (not necessity) to be included alongside with the experiments you run in a joint journal publication. If this is something that might interest you, please reach out to me at gcorso at https://t.co/VkKWACM16p or DM me on the boltz-community Slack!

[Daniel Alvarez @daninthenet]

So… I’ve just learned some of my repos are buried in an arctic vault 🤯

[LaurieWired @lauriewired]

If you see a github user with this badge it’s because they have code ~1,000 feet underground in the Arctic Circle.

5 years ago Github took a snapshot of all public repos, stored it on photographic film (essentially big QR codes), and stuck it in a mining tunnel.

[Anthropic @AnthropicAI]

New Anthropic Research: Project Vend.

We had Claude run a small shop in our office lunchroom. Here’s how it went.

[hardmaru @hardmaru]

New Paper: Continuous Thought Machines 🧠

Neurons in brains use timing and synchronization in the way that they compute, but this is largely ignored in modern neural nets. We believe neural timing is key for the flexibility and adaptability of biological intelligence.

We propose a new neural architecture, “Continuous Thought Machines” (CTMs), which is built from the ground up to use neural dynamics as a core representation for intelligence. By using neural dynamics as a first-class representational citizen, CTMs naturally perform adaptive computation.

Many emergent, interesting behaviors arise as a result: CTMs solve mazes by observing a raw maze image and producing step-by-step instructions directly from its neural dynamics. When tasked with image recognition, the CTM naturally takes multiple steps to examine different parts of the image before making its decision. This step-by-step approach not only makes its behavior more interpretable but also improves accuracy: the longer it “thinks,” the more accurate its answers become.

We also found that this allows the CTM to decide to spend less time thinking on simpler images, thus saving energy. When identifying a gorilla, for example, the CTM’s attention moves from eyes to nose to mouth in a pattern remarkably similar to human visual attention.

I think this work underscores an important, yet often lost, synergy between neuroscience and AI. While modern AI is ostensibly brain-inspired, the two fields often operate in surprising isolation. By starting with such inspiration and iteratively following the emergent, interesting behaviors, we developed a model with unexpected capabilities, such as its surprisingly strong calibration in classification tasks, a feature that was not explicitly designed for.

When we initially asked, “why do this research?”, we hoped the journey of the CTM would provide compelling answers. By embracing light biological inspiration and pursuing the novel behaviors observed, we have arrived at a model with emergent capabilities that exceeded our initial designs. We are committed to continuing this exploration, borrowing further concepts to discover what new and exciting behaviors will emerge, pushing the boundaries of what AI can achieve.

[Daniel Alvarez @daninthenet]

@tomkrcha Would love to try!

[Daniel Alvarez @daninthenet]

@iwatobipen Exciting times!

[Daniel Alvarez @daninthenet]

Anyone knows of any opensource/free tool for conformer generation faster than rdkit? And any more accurate? Or BOTH?!?!?! 🥲 #compchem #chemtweeter #sbdd #modeling

[lewis martin @lewischewis]

this paper is sooo good. boils down to 'what if I just simulate at 1000 degrees and see how long each ligand can hold on for?' and it works

[Daniel Alvarez @daninthenet]

@DdelAlamo I believe this is the standard behaviour in all MD simulation engines. During trajectory analysis you can align and “wrap” all the atoms in a single periodic box unit. Certain properties (e.g. diffusion coefficients) can only be calculated before “wrapping”.

[Daniel Alvarez @daninthenet]

@TheProjectUnity Figure I is a thermal image messuring body surface temperature, nothing to do with photons nor meditation states. Info in the source article: https://t.co/2tgANq3eF4

[Daniel Alvarez @daninthenet]

Cool new application of mixed solvent MDs for the identification of ligand exit pathways #compchem #mdmix

https://t.co/UR21n2tkYD

[Daniel Alvarez @daninthenet]

Great editorial by Tudor Oprea and David Weininger: “Rethinking Medicinal Chemistry in the Cheminformatics Age” #medchem #compchem #cheminfo

https://t.co/zL8wktLuWY

[Sam Rodriques @SGRodriques]

Introducing PaperQA2, the first AI agent that conducts entire scientific literature reviews on its own.

PaperQA2 is also the first agent to beat PhD and Postdoc-level biology researchers on multiple literature research tasks, as measured both by accuracy on objective benchmarks and assessments by human experts. We are publishing a paper and open-sourcing the code.

This is the first example of AI agents exceeding human performance on a major portion of scientific research, and will be a game-changer for the way humans interact with the scientific literature.

Paper and code are below, and congratulations in particular to @m_skarlinski, @SamCox822, @jonmlaurent, James Braza, @MichaelaThinks, @mjhammerling, @493Raghava, @andrewwhite01, and others who pulled this off. 1/

[Daniel Alvarez @daninthenet]

Excellent read! right on point.

[Eric Dai @EricDai_BioE]

https://t.co/LITcgWL28J

[Daniel Alvarez @daninthenet]

@deedydas 🤣

[Daniel Alvarez @daninthenet]

I usually draw several molecules in Marvin Sketch and it is later a pain to save them independently in a single SDF file. I found a shortcut: Save to CXSMILES, use BASH + @OpenBabel_org
#bashgeek #openbabel #bash #compchemtips #compchem