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Jess White

@jessbwhite.bsky.social

Current: Tri-I CBM student in @jchodera@bsky.social and Wesley Tansey labs Previous: SWTX | OrbiMed | WeillCornellGS | BofAML | Penn | Andover Employer-mandated disclaimer: choderalab.org/disclaimer

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Jess White@jessbwhite.bsky.social · 6mo ago

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

bioRxiv Cancer Bio@biorxiv-cancer.bsky.social · 6mo ago

A Pan-Cancer Ex Vivo Drug Screen Atlas for Functional Precision Oncology https://www.biorxiv.org/content/10.64898/2026.02.14.705918v1

John Chodera@jchodera.bsky.social · 7mo ago

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

Home | openbind.uk

openbind.ai

OpenBind@openbind.bsky.social · 7mo ago

Join our mailing list for early access to AI-driven drug discovery insights & breakthroughs through the #OpenBind initiative. https://loom.ly/Vro7Lo8

Jess White@jessbwhite.bsky.social · 8mo ago

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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Popehat@kenwhite.bsky.social · last yr.

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.

The New York Times@nytimes.com · last yr.

The killings of two Israeli Embassy workers in Washington on Wednesday cast a harsh spotlight on the pro-Palestinian movement in the U.S. and the impact even peaceful protests might be having on attitudes against people connected to Israel.

Jess White@jessbwhite.bsky.social · last yr.

Grateful for the opportunity to present my work to such an engaged audience! Find out more here: bit.ly/4kcOQnX #Kinase2025

GitHub - choderalab/missense-kinase-toolkit: A package to facilitate structure- and sequence-based ML for clinically relevant missense human kinase property prediction

A package to facilitate structure- and sequence-based ML for clinically relevant missense human kinase property prediction - choderalab/missense-kinase-toolkit

bit.ly

Mark Polk@markpolk.io · last yr.

In Edinburgh for the RSC/SCI Symposium on Kinase Inhibitor Design—excited to see @jessbwhite.bsky.social share her work on the missense kinase toolkit! #Kinase2025

Jess White@jessbwhite.bsky.social · last yr.

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...

Reinstate funding for pandemic prevention research and preparedness

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

resist.bot

Reuters@reuters.com · last yr.

The US Department of Health and Human Services canceled around $12 billion in federal grants to states that were allocated during the COVID-19 pandemic. The grants were being used to track, prevent and control infectious diseases, said lawmakers reut.rs/41WVed3

Sukrit Singh@sukritsingh92.bsky.social · last yr.

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.
Sukrit Singh@sukritsingh92.bsky.social · 2y ago

New preprint! We prospectively evaluate structure-based methods and measure how well they classify clinical kinase mutations as inhibitor–resistant or –sensitizing when compared against our NanoBRET assay. Alchemical methods are well-suited to modeling distal mutants! Link: doi.org/10.1101/2024...

John Chodera@jchodera.bsky.social · last yr.

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.
Roland Dunbrack 🏳️‍🌈@rolanddunbrack.bsky.social · last yr.

🧵 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.

TM equation of Zhang and Skolnick
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · last yr.

Res ipSAE loquunt: What's wrong with AlphaFold's ipTM score and how to fix it https://www.biorxiv.org/content/10.1101/2025.02.10.637595v1

Carl T. Bergstrom@carlbergstrom.com · last yr.

1. Today the NIH director issued a new directive slashing overhead rates to 15%. I want to provide some context on what that means and why it matters. grants.nih.gov/grants/guide...

NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates

NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD

grants.nih.gov

Jess White@jessbwhite.bsky.social · 2y ago

Happy to have been a member of the BATCHIE team who worked on this recent publication featured by @MSKLibrary: A Bayesian active learning platform for scalable combination drug screens dx.doi.org/10.1038/s414...

A Bayesian active learning platform for scalable combination drug screens - Nature Communications

Large-scale combination drug screens in cancer are extremely challenging because of the immense number of possible combinations. Here, the authors develop BATCHIE, a Bayesian active learning platform ...

dx.doi.org

Gabriele Corso@gcorso.bsky.social · 2y ago

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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