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David L. Dotson @dotsdl.bsky.social · Jun 3

Earlier this year we released alchemiscale v0.6.0, and followed this up with v0.6.1 and v0.6.2. We wanted to take a moment to highlight these releases, and the improvements they bring for users!

Read our full post here: alchemiscale.org/advancements...

#compchem #drugdiscovery #alchemistry

advancements in alchemiscale v0.6

In February of this year we released alchemiscale v0.

alchemiscale.org

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David L. Dotson @dotsdl.bsky.social · May 27

Eager to apply alchemiscale and @openfree.energy to your problems, but not sure where to start? Don't hesitate to reach out!

#compchem #alchemistry #opensource #openscience

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David L. Dotson @dotsdl.bsky.social · May 27

This poster illustrates the substantial flexibility of the open source @openfree.energy ecosystem, enabling unconventional approaches for applying free energy methods. As this ecosystem continues to evolve, I'm excited to see what users do with the advancements we make!

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David L. Dotson @dotsdl.bsky.social · May 27

With alchemiscale as the coordinator and Folding@Home as a "planetary scale" engine of citizen-science compute, we are able to increase our calculation throughput by at least 3x over conventional compute alone, and with equal accuracy!

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David L. Dotson @dotsdl.bsky.social · May 27

Proud to have shared some of our recent work at the 2025 Workshop on Free Energy Methods in Boston!

Our poster detailed the engineering approach we took to enable large-scale computation of alchemical binding free energies via alchemiscale (alchemiscale.org) and Folding@Home (foldingathome.org).

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Reposted by David L. Dotson

Jen Mercieca @jenmercieca.bsky.social · May 11

If they suspend Habeas Corpus, it won't just be for "migrants" or "illegals" or "criminals." If they suspend Habeas Corpus it will be for you and me and whomever this regime decides is unfit, undesirable, and a threat or a problem. This is how it works. This is how it's always worked.

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David L. Dotson @dotsdl.bsky.social · May 5

En route to Boston for the 2025 Workshop on Free Energy Methods in Drug Design!

Looking for ways to better scale the free energy calculations that support your active drug discovery programs? Hit me up here or find me there!

#drugdesign #drugdiscovery #compchem #alchemistry

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David L. Dotson @dotsdl.bsky.social · Apr 21

Excited to announce that Achira (achira.ai) is supporting Datryllic in advancing alchemiscale in 2025!

Details here: alchemiscale.org/advancements...

Looking to scale free energy calculations for your applications? Don’t hesitate to reach out!

#drugdiscovery #alchemistry #opensource #compchem

Achira support for Datryllic's efforts in 2025

In February, we published the alchemiscale project’s 2025 roadmap, detailing our objectives for the year, our available resources, and the path we intend to take to leverage these resources in service...

alchemiscale.org

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David L. Dotson @dotsdl.bsky.social · Mar 19

Yup. The US is really cutting off its nose to spite its face here, and abdicating its own position as a global leader in scientific advancement.

It's beyond stupid.

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Reposted by David L. Dotson

John Chodera @jchodera.bsky.social · Feb 19

Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed:

Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.

Figure 1 from arXiv preprint https://doi.org/10.1101/2025.01.06.631610

Fig. 1 Espaloma is an end-to-end differentiable molecular mechanics parameter assignment scheme for arbitrary organic molecules. Espaloma (extensible surrogate potential optimized by message-passing) is a modular approach for directly computing molecular mechanics force field parameters FFF from a chemical graph G such as a small molecule or biopolymer via a process that is fully differentiable in the model parameters FNN. In Stage 1, a graph neural network is used to generate continuous latent atom embeddings describing local chemical environments from the chemical graph. In Stage 2, these atom embeddings are transformed into feature vectors that preserve appropriate symmetries for atom, bond, angle, and proper/improper torsion inference via Janossy pooling.54 In Stage 3, molecular mechanics parameters are directly predicted from these feature vectors using feed-forward neural networks. This parameter assignment process is performed once per molecular species, allowing the potential energy to be rapidly computed using standard molecular mechanics or molecular dynamics frameworks thereafter. The collection of parameters FNN describing the espaloma model can be considered as the equivalent complete specification of a traditional molecular mechanics force field such as GAFF38,39/AM1-BCC55,56 in that it encodes the equivalent of traditional typing rules, parameter assignment tables, and even partial charge models. Reproduced from ref. 49 with permission from the Royal Society of Chemistry.

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David L. Dotson @dotsdl.bsky.social · Feb 17

Guess I'll start using the great American high speed rail...

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David L. Dotson @dotsdl.bsky.social · Feb 12

"But the price of eggs!" is the new "But her emails!" 🫠

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David L. Dotson @dotsdl.bsky.social · Feb 12

This month the alchemiscale project celebrates its 3rd anniversary since kicking off in 2022! We've come a long way, and there is much we look forward to improving this year.

Read about where we're going in 2025: alchemiscale.org/roadmaps/alc...

#compchem #opensource #alchemistry #drugdiscovery

alchemiscale roadmap 2025

It’s 2025, and this month the project now known as alchemiscale celebrates its 3rd anniversary since kicking off in 2022.

alchemiscale.org

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David L. Dotson @dotsdl.bsky.social · Jan 30

Ah yes, the DEI boogeyman strikes again. 🙄

David L. Dotson @dotsdl.bsky.social · Jan 24

Very pleased to announce that ASAP Discovery (asapdiscovery.org) is supporting Datryllic in advancing alchemiscale in 2025!

More details here: alchemiscale.org/advancements...

Looking to advance alchemiscale further? Don’t hesitate to reach out!

#drugdiscovery #alchemistry #opensource #compchem

Datryllic efforts for ASAP Discovery in 2025

In October, we offered a detailed perspective on what we considered to be the alchemiscale project’s most attractive advancement opportunities in 2025.

alchemiscale.org

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David L. Dotson @dotsdl.bsky.social · Jan 8

Ask Poland about how entitled Germany felt to its land less than a century ago. Lebensraum and all that.

David L. Dotson @dotsdl.bsky.social · Jan 8

Ego-driven policy, blatant oligarchy, and ecological disaster we may never recover from.

David L. Dotson @dotsdl.bsky.social · Jan 1

It had me at space elevator. 😍

David L. Dotson @dotsdl.bsky.social · Dec 30

Tis the season for making space to realign the spirit with the mind and body.

To rekindle the enthusiasm that set you down the path you're on, and to consider the possibilities beyond it.

To take stock of what you have learned, and what you likely need to.

To be ready to make a positive impact.

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Reposted by David L. Dotson

Polaris @polarishub.io · Dec 3

🦠 We’re excited to announce our first competition in partnership with @asapdiscovery.bsky.social and @omsf.io!

Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵

Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...

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Reposted by David L. Dotson

John Chodera @jchodera.bsky.social · Nov 16

The OMSF (@omsf.bsky.social) OpenADMET project is hiring a Science Lead for ML models of molecular property prediction, as well as a Senior Scientist for data curation and pipeline integration! Help build the future of open source ADMET prediction and ML model enablement!

openadmet.org/jobs/

openadmet.org

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Reposted by David L. Dotson

OMSF @omsf.io · Sep 28

We are now on Bluesky! OMSF supports the ever-growing ecosystem of open source molecular software. We love all things #opensource, #science, and #software - if you do too, follow us!

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David L. Dotson @dotsdl.bsky.social · Nov 14

@katyhuff.bsky.social howdy stranger! Great to see you here!

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David L. Dotson @dotsdl.bsky.social · Nov 12

To all the newcomers to @bsky.app , welcome! Let's make this a better place than, well, you already know. 😁

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