Nate
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natehstanley.bsky.social
Nate
@natehstanley.bsky.social
55 followers 200 following 2 posts
Interested in helping cure diseases; machine learning for chemistry and biology
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Reposted by Nate
pwk2024.bsky.social
Opportunity for computational chemist at Inductive Bio (USA: New York City, San Francisco, or Boston) #CompChem #cheminformatics #ADMET #ChemJobs #chemsky 🧪
www.inductive.bio/careers?ashb...
We're Hiring | Inductive Bio
Inductive Bio is accelerating small molecule drug discovery with cutting-edge AI and proprietary data. Join our fast-growing team backed by top investors like a16z and Lux.
www.inductive.bio
October 23, 2025 at 6:14 AM
Reposted by Nate
cryptogenomicon.bsky.social
Yes, this is accurate.
October 21, 2025 at 6:29 PM
Reposted by Nate
chemjobber.bsky.social
Is this accurate?!? Re Harvard CCB

"Chemistry and Chemical Biology will go down to four or five admits, one of the professors added."
jbenmenachem.com jon ben-menachem @jbenmenachem.com · 25d
Wow. Harvard nuking its PhD programs

- Science PhD admissions reduced by more than 75%
- Arts & Humanities reduced by about 60%
- Social Sciences by 50–70%
- History by 60%
- Biology by 75%
- The German department will lose all PhD seats
- Sociology from six PhD students to zero
Harvard FAS Cuts Ph.D. Seats By More Than Half Across Next Two Admissions Cycles | News | The Harvard Crimson
The Faculty of Arts and Sciences slashed the number of Ph.D. student admissions slots for the Science division by more than 75 percent and for the Arts & Humanities division by about 60 percent for th...
www.thecrimson.com
October 21, 2025 at 6:26 PM
Reposted by Nate
lindorfflarsen.bsky.social
We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale

See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs

📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...
Figure showing the AF-CALVADOS restraining and simulation protocol based on AF2 structure, PAE and pLDDT
October 20, 2025 at 11:26 AM
Reposted by Nate
adrianroitberg.bsky.social
If you used our ANI MLIPs, you probably used our TorchANI library. Now, new and improved version 2.0. Use it, enjoy it, break it, let us know what you did or tried to do with it. doi.org/10.1021/acs.jcim.5c01853
@ignaciopickering.bsky.social @nickterrel.bsky.social @khuddleston.bsky.social
TorchANI 2.0: An Extensible, High-Performance Library for the Design, Training, and Use of NN-IPs
In this work, we introduce TorchANI 2.0, a significantly improved version of the free and open source TorchANI software package for training and evaluation of ANI (ANAKIN-ME) deep learning models. Tor...
pubs.acs.org
October 17, 2025 at 9:32 PM
Reposted by Nate
benblaiszik.bsky.social
🔥We're excited to announce a major milestone for the machine-learned interatomic potential (MLIP) ecosystem: TorchSim is moving to community ownership and governance through a partnership with Radical AI and the open-source community! TorchSim is an atomistic simulation engine built for the AI era.
October 15, 2025 at 7:06 PM
Reposted by Nate
xuhuihuangchem.bsky.social
I received many requests to share materials from our undergraduate course “Machine Learning in Chemistry”
— here you go!

A preprint summarizing insights and lessons learned:
chemrxiv.org/engage/chemr...

A Jupyter Notebook Tutorial Gallery:
xuhuihuang.github.io/mlchem/html/...
October 16, 2025 at 1:27 AM
Reposted by Nate
carlzimmer.com
Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE
nyti.ms
October 8, 2025 at 11:29 PM
Reposted by Nate
janhjensen.bsky.social
My talk at the #RDKit UGM in Prague youtu.be/TduH7v-biyY?... #compchem
Jan Jensen: Can you find hits by screening only 100 molecules?
YouTube video by RDKit
youtu.be
October 5, 2025 at 9:09 AM
Reposted by Nate
krhornberger.bsky.social
Discovery of a New and Selective HPK1 PROTAC for Enhancing Tumor Immunotherapy through Eliminating GLK Degradation
Discovery of a New and Selective HPK1 PROTAC for Enhancing Tumor Immunotherapy through Eliminating GLK Degradation
HPK1 is an attractive therapeutic target for tumor immunotherapy. Nevertheless, the formidable challenge selectivity over GLK and limited antitumor efficacy of HPK1 inhibitors and PROTACs impeded thei...
pubs.acs.org
June 11, 2025 at 11:01 AM
Reposted by Nate
smcgrath.phd
🧪In a JAMA viewpoint paper, the FDA expresses its intent to use AI for first-pass reviews of drug applications to significantly increase efficiency.

This is premature and we haven't seen the evidence AI is ready for this use case.

Link to the paper: jamanetwork.com/journals/jam...

#MedSky #MLSky
F.D.A. to Use A.I. in Drug Approvals to ‘Radically Increase Efficiency’
With a Trump-driven reduction of nearly 2,000 employees, agency officials view artificial intelligence as a way to speed drugs to the market.
www.nytimes.com
June 10, 2025 at 9:11 PM
Reposted by Nate
anthonyc1nash.bsky.social
Force fields with QM accuracy and MM speed are the theoretical biophysicist's Philosopher's Stone. I used ANIX2 with OpenFF and OpenMM. The results were insightful but at the expense of huge computational costs. #MLFF #biophysics #moleculardynamics
On the design space between molecular mechanics and machine learning force fields
A force field as accurate as quantum mechanics (QMs) and as fast as molecular mechanics (MMs), with which one can simulate a biomolecular system efficiently eno
pubs.aip.org
April 5, 2025 at 10:48 AM
Reposted by Nate
chaitjo.bsky.social
Sharing slides for All-atom Diffusion Transformers

- briefly summarises the big ideas and key takeaways

Link - www.chaitjo.com/publication/...
April 4, 2025 at 5:40 PM
natehstanley.bsky.social
Man, I gotta say, @aspuru.bsky.social definitely made the right choice to bail on the US way back in 2018. I mean I understood back then, but... prescient decision!!
April 5, 2025 at 4:31 AM
Reposted by Nate
jchodera.bsky.social
Incredibly grateful to have helped build the ASAP Discovery Consortium (@asapdiscovery.bsky.social) that enabled @griffen-ed.bsky.social and all the other amazing members of this team to discover a new broad-spectrum coronavirus antiviral!
asapdiscovery.bsky.social The ASAP Discovery Consortium @asapdiscovery.bsky.social · Mar 21
Lead medicinal chemist Ed Griffen (@griffen-ed.bsky.social) will be disclosing the new ASAP MERS-CoV/SARS-CoV-2 oral antiviral at @acs.org on Tue 25 Mar! Tune in to this virtual session to hear about its discovery and development!

acs.digitellinc.com/live/34/sess...
ACS talk 4181593 - Discovery of non-peptidomimetic oral combined MERS and SARS-CoV-2 anti-virals Presented by Ed Griffen Part of the session "Developing Countermeasures for Viruses of Pandemic Potential" Room: Digital Session (Digital Meeting) Overview: The COVID-19 pandemic was a stark reminder that a barren global antiviral pipeline has grave humanitarian consequences. Pandemics could be prevented, in principle, by accessible, easily deployable broad-spectrum oral antivirals. Here we report the discovery of a family non-peptidomimetic spirolactams that target critical pathogenic coronaviridae including SARS-CoV-2 and MERS-CoV. As part of the ASAP AViDD centre(www.asapdiscovery.org) we expanded the work of the COVID Moonshot's drug discovery campaign targeting the SARS-CoV-2 main protease to deliver orally active compounds with promising in vivo profiles. Using a combination of active learning based medicinal chemistry, alchemical free energy calculations and structure-based design we were able to extend the coronavirus spectrum and optimise the ADMET properties of the series leading to the first public disclosure of the preclinical candidate.
March 21, 2025 at 4:58 PM
Reposted by Nate
aspuru.bsky.social
Chemistry is changed by AI at a super rapid pace! Check our data miner for chemical reactions, MERMaid!

@accelerationc.bsky.social @thematterlab.bsky.social @shixuanleong.bsky.social #chemsky #compchemski #ai #vlm #llm #aiforscience Please follow @thematterlab.bsky.social
March 14, 2025 at 11:34 PM
Reposted by Nate
rommieamaro.bsky.social
What an awesome group effort reporting on the structural dynamics of ~60% of available structures !!

www.nature.com/articles/s41...
March 2, 2025 at 5:18 PM
Reposted by Nate
prasad.bsky.social
not just NIH websites
March 2, 2025 at 12:43 AM
Reposted by Nate
pergamic.bsky.social
The next step in trying to dismantle Infectious Diseases research - dismantle @niaidnews.bsky.social - should surprise no one that this a R-led proposal.

An unmitigated disaster for diagnosis, treatment and prevention of pathogens that affect everyone in the US

www.congress.gov/bill/119th-c...
www.congress.gov
February 22, 2025 at 7:55 PM
Reposted by Nate
chaitjo.bsky.social
Our first attempts at mechanistic interpretability of Transformers from the perspective of network science and graph theory!

A wonderful collaboration with superstar MPhil students Batu El, Deepro Choudhury, as well as Pietro Liò as part of the Geometric Deep Learning class at @cst.cam.ac.uk
February 19, 2025 at 11:57 AM
Reposted by Nate
olgatticus.bsky.social
Variational Flow Matching goes Riemannian! 🔮

In this preliminary work, we derive a variational objective for probability flows 🌀 on manifolds with closed-form geodesics, and discuss some interesting results.

Dream team: Floor, Alison & Erik (their @ below) 💥

📜 arxiv.org/abs/2502.12981
🧵1/5
February 19, 2025 at 3:13 PM
Reposted by Nate
zenbrainest.bsky.social
WOW!!
De novo design of transmembrane fluorescence-activating proteins
www.nature.com/articles/s41...
De novo design of transmembrane fluorescence-activating proteins - Nature
A study describes the design of de novo ligand-binding transmembrane proteins, demonstrating their specific binding and activation of fluorogenic ligands.
www.nature.com
February 19, 2025 at 4:48 PM
Reposted by Nate
jchodera.bsky.social
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.
February 19, 2025 at 7:30 PM
Reposted by Nate
franknoe.bsky.social
The BioEmu-1 model and inference code are now public under MIT license!!!

Please go ahead, play with it and let us know if there are issues.

github.com/microsoft/bi...
February 19, 2025 at 8:17 PM