iiinova — where your digital self keeps evolving

Reposted by Jess White

bioRxivpreprint @biorxivpreprint.bsky.social · 18/09/2026

Physical priors improve performance of structure-based binding affinity models www.biorxiv.org/content/10.64898/20…

Reposted by Jess White

Sukrit Singh @sukritsingh92.bsky.social · 07/07/2026

New preprint! Do all kinase domains have similar activation mechanisms? We steer AlphaFold2 using "transfer seeding" of known kinases to sample 8.3 ms of MD simulations via Folding@home. We find unique pathways that are kinase-specific and depend on different elements! Link: doi.org/10.64898/202...

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Reposted by Jess White

Sukrit Singh @sukritsingh92.bsky.social · 02/04/2026

More protein-ligand data are needed for AlphaFold-like models (& AI/ML) to enable prospective design! Check out our piece in "Current Opinion in Structural Biology" – Equal parts a thank-you-letter to the PDB & summarizes how datasets will enable task-focused models! Link: doi.org/10.1016/j.sb...

Diagram titled ‘Protein–Drug Prediction Task Breakdown’ showing a hierarchical tree of modeling tasks. Top branches include apo monomer and protein–protein interactions, with sub-branches such as ensembles, induced-fit models, multimers, folded–unfolded complexes, and protein–ligand complexes with mutation effects on binding. Additional branches include potency, ADMET properties (e.g., solubility and blood–brain barrier penetration), and kinetics (e.g., koff). A legend indicates model maturity levels: solid lines (established), dashed lines (promising), and dotted lines (untapped).

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Reposted by Jess White

Diego del Alamo @delalamo.xyz · 25/02/2026

We're hiring - looking for folks with experience designing and training foundation models from scratch, particularly biomolecular language models, GNNs, or vision models. Lots of room for creativity in this role. Contact me if you have any interest

jobs.takeda.com

Research Senior Scientist AI/ML Foundational Models at Takeda Pharmaceutical

Learn more about applying for Research Senior Scientist AI/ML Foundational Models at Takeda Pharmaceutical

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Reposted by Jess White

AI x Bio Discovery @aixbiobot.bsky.social · 20/02/2026

Defining the Active Conformation of Typical Protein Kinases Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases [new]

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Jess White @jessbwhite.bsky.social · 18/02/2026

Pleased to share our preprint from the Tansey lab at @mskcancercenter.bsky.social: the Pan-PreClinical (PPC) project. To mitigate biases in immortalized cell line screens, we curated an atlas of >2M experiments in ~2k patient-derived ex vivo constructs using 3k+ drugs. Interactive web portal here

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Reposted by Jess White

John Chodera @jchodera.bsky.social · 12/01/2026

OpenBind is a new open science effort to dramatically increase the number of protein:ligand structures in the PDB, pairing this with high-quality affinity data to enable a new generation of predictive structure and affinity models for drug discovery. Check it out: openbind.ai

openbind.ai

Home | openbind.uk

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Jess White @jessbwhite.bsky.social · 12/12/2025

I want to extended my gratitude to my advisors, @jchodera.bsky.social and Wesley Tansey, for their continued guidance and support. And a special thank you to fellow Chodera Team Kinase colleagues @sukritsingh92.bsky.social and @markpolk.io.

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Jess White @jessbwhite.bsky.social · 12/12/2025

I'm honored to share that I've been selected as a 2026 PhRMA Foundation Predoctoral Fellow in Drug Discovery. This fellowship will support my research assessing how clinically relevant missense mutations impact kinase activity. Read more about our work here.

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Reposted by Jess White

Achira @achira-ai.bsky.social · 24/10/2025

Achira is growing! We’re looking for talented software engineers, ML research engineers, and AI/ML scientists to join our team in building foundation simulation models to power the future of drug discovery. Apply at achira.ai

achira.ai

Achira

Building foundation simulation models for drug discovery

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Reposted by Jess White

AI x Bio Discovery @aixbiobot.bsky.social · 25/09/2025

How many crystal structures do you need to trust your docking results? [new] Accurate drug docking needs crystal struct. Template docking via mol. similarity helps w/ ltd. data.

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Reposted by Jess White

Anshul Kundaje @anshulkundaje.bsky.social · 19/08/2025

@jengreitz.bsky.social l & my lab want to co-hire a computational biologist/biostatistician with project management expertise to help map the regulatory code of the human genome and discover genetic mechanisms of disease. Details below careersearch.stanford.edu/jobs/computa... Plz RT

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Reposted by Jess White

mia @miarosenfeld.bsky.social · 22/07/2025

pls RT for reach! can’t wait to see y’all there 😁 @acs.org #CompChem

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Reposted by Jess White

Popehat @kenwhite.bsky.social · 23/05/2025

The steady deterioration of First Amendment rights and the conflation of violence with dissent is a result not just of an authoritarian regime but of a press culture that is feckless at best and authoritarian-fluffers at worst. The New York Times is beyond redemption.

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Jess White @jessbwhite.bsky.social · 11/04/2025

This could be incredibly dangerous

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Jess White @jessbwhite.bsky.social · 27/03/2025

Communicate your opposition to the cancelation of billions of dollars in pandemic preparedness grants to all of your elected representatives simultaneously here: resist.bot/petitions/PX...

resist.bot

Reinstate funding for pandemic prevention research and preparedness

Text SIGN PXNIDH to 50409 to send this to your officials.

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Reposted by Jess White

Seth Rockman @sethrockman.bsky.social · 19/03/2025

In honor of #MarchMadness, let's talk about how all 8 men's teams playing in Providence this week are threatened by the Musk/Trump Admin. If you love college sports, you're going to have to stand up for colleges!!!!

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Reposted by Jess White

Sukrit Singh @sukritsingh92.bsky.social · 10/03/2025

This work is now published in J Phys Chem B! Check out our work showing that simulations predict the impact of distal mutations on kinase-inhibitor binding, and our experimental NanoBRET dataset of 94 kinase mutations that provide a benchmark for future methods. Link: pubs.acs.org/doi/full/10....

Illustration showing a pipeline for predicting the impact of ABL1A kinase domain mutations on inhibitor binding. On the left, icons labeled 'Physics-based simulations' and 'Data-driven methods' feed into 'Prospective ΔΔG Predictions.' On the right, a 3D ribbon model of the ABL1A kinase domain (gray) highlights clinically observed mutations in orange and an inhibitor in blue.

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Reposted by Jess White

Eric Topol @erictopol.bsky.social · 01/03/2025

Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter www.nytimes.com/2025/03/01/u...

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Reposted by Jess White

John Chodera @jchodera.bsky.social · 19/02/2025

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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Reposted by Jess White

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 16/02/2025

🧵 on our preprint: Zhang & Skolnick's TM score for comparing model of protein to experimental structures of same protein. The d_j are essentially the same as the aligned error in Alphafold. After any structure alignment, it's the displacement of model Calpha from experimental Calpha of residue j.

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Reposted by Jess White

Mark Polk @handle.invalid · 16/02/2025

Excited to be in LA for #BPS2025 @biophysicalsoc.bsky.social! I’ll be presenting a poster on our high-throughput fluorescence-based assay for kinase inhibitor binding in the West Exhibit Hall on Monday at 2:45 PM (board B60).

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Reposted by Jess White

Sukrit Singh @sukritsingh92.bsky.social · 16/02/2025

I'll be presenting my work prospectively studying clinical mutations and their impact on kinase inhibitor binding at #bps2025! Come see my talk on Wednesday morning @ 8:45am.

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Reposted by Jess White

David A Knowles @davidaknowles.bsky.social · 27/01/2025

#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!

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Reposted by Jess White

Polaris @polarishub.io · 14/01/2025

🏁 The antiviral challenge is live! 🏁 Ready to test your skills on new data? Hosted in partnership with @asapdiscovery.bsky.social and @omsf.io, we've prepared detailed notebooks showcasing how to format your data and submit your solutions. 🧑‍💻

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Reposted by Jess White

Polaris @polarishub.io · 03/12/2024

🦠 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 Jess White

Mark Polk @handle.invalid · 27/11/2024

Automated plate handling in the Chodera Lab, part of our effort to study kinase inhibitors in high throughput.

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Reposted by Jess White

Gabriele Corso @gcorso.bsky.social · 17/11/2024

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

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Reposted by Jess White

Walker Bragman @walkerbragman.bsky.social · 16/11/2024

Here’s another critical piece of info about Bhattacharya: Multiple judges in court cases over COVID mitigations where he’s been been used as an expert have called his expertise into question. www.importantcontext.news/p/judges-kee...

importantcontext.news

Judges Keep Questioning Herd Immunity Advocate’s Credibility

"At this stage of the proceedings, the Court is simply unwilling to trust Dr. Bhattacharya."

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Reposted by Jess White

Brendan Nyhan @brendannyhan.bsky.social · 15/11/2024

This article is totally insane; NPR should be ashamed. The headlines and lede give you no indication at all that RFK is a crank whose claims about vaccines are false and threaten public health. Would they write a story saying "Alex Jones wants to inform the public but he faces a lot of pushback"?

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