David L. Dotson

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

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

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!

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!

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).

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.

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

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

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.

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.

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.

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

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

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

Ah yes, the DEI boogeyman strikes again. 🙄

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.

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

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

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

It had me at space elevator. 😍

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.

🦠 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...

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/

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!

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

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

Do you use alchemiscale in production? Or would you like to?

We recently shared a perspective on the progress of the project, where we're currently focused, and the opportunities we see for advancement in 2025:

alchemiscale.org/opportunitie...

Let us know what you think! #drugdiscovery #oss

Gave an invited talk a few weeks back at Memorial Sloan Kettering Cancer Center on alchemiscale (github.com/openforcefie...), and how we're working to scale out alchemical free energy calculations to support open data antiviral discovery for ASAP Discovery (asapdiscovery.org) via Folding@Home.