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Jess White

@jessbwhite.bsky.social

180 followers 600 following 18 posts

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Jess White @jessbwhite.bsky.social · May 13

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

Reposted by Jess White

AI x Bio Discovery @aixbiobot.bsky.social · 17d

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 · Aug 19

@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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Jess White @jessbwhite.bsky.social · Aug 17

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mia @miarosenfeld.bsky.social · Jul 22

pls RT for reach! can’t wait to see y’all there 😁

@acs.org #CompChem

acscomp.bsky.social @acscomp.bsky.social · Jul 22

Mark your calendars for the ACS COMP *SUNDAY* Social on August 17, 2025! Free German 🥨&🍻 for COMP members, sponsored by OpenEye + Cadence 💻

RSVP link dropping soon in all ACS COMP members' email inboxes :)

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Jess White @jessbwhite.bsky.social · Jul 4

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Jess White @jessbwhite.bsky.social · Jul 1

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Jess White @jessbwhite.bsky.social · Jun 18

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Jess White @jessbwhite.bsky.social · Jun 15

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Jess White @jessbwhite.bsky.social · Jun 11

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Reposted by Jess White

Old White Nepo Hat @kenwhite.bsky.social · May 23

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 · May 23

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.

Pro-Palestinian Movement Faces an Uncertain Path After Embassy Attack

www.nytimes.com

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Jess White @jessbwhite.bsky.social · May 13

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

Jess White @jessbwhite.bsky.social · Apr 20

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Jess White @jessbwhite.bsky.social · Apr 11

This could be incredibly dangerous

boehninglab @boehninglab.com · Apr 11

This is chilling www.fda.gov/news-events/...

FDA Announces Plan to Phase Out Animal Testing Requirement for Monoclonal Antibodies and Other Drugs

FDA Plans to Phase Out Animal Testing Requirement

www.fda.gov

Jess White @jessbwhite.bsky.social · Apr 5

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Jess White @jessbwhite.bsky.social · Mar 27

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...

Reposted by Jess White

Seth Rockman @sethrockman.bsky.social · Mar 19

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 · Mar 10

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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Jess White @jessbwhite.bsky.social · Mar 15

Musk Said No One Has Died Since Aid Was Cut. That Isn’t True. www.nytimes.com/interactive/...

Opinion | Musk Said No One Has Died Since Aid Was Cut. That Isn’t True. (Gift Article)

A journey through the front lines of global poverty shows that when the world’s richest men slash aid for the world’s poorest children, the result is sickness, starvation and death.

www.nytimes.com

Reposted by Jess White

Eric Topol @erictopol.bsky.social · Mar 1

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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Jess White @jessbwhite.bsky.social · Feb 22

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Reposted by Jess White

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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Reposted by Jess White

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · Feb 16

🧵 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 @markpolk.io · Feb 16

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 · Feb 16

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

Carl T. Bergstrom @carlbergstrom.com · Feb 8

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

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