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Reposted by Sukrit Singh

bioRxiv Biophysics @biorxiv-biophys.bsky.social · 17d

How many crystal structures do you need to trust your docking results? https://www.biorxiv.org/content/10.1101/2025.09.19.677428v1

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Reposted by Sukrit Singh

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 Sukrit Singh

Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · 26d

DYK: 76% of MSK postdoctoral researchers are international, coming from more than 60 countries for training and mentorship that translates into scientific discoveries across the globe? 🌎 Learn more about our incredible MSK postdocs:

#PostdocAppreciationWeek

International Postdocs From 60 Countries Are Training at MSK in 2025

What inspires the outstanding young scientists who come from around the world to train at MSK?

www.mskcc.org

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Sukrit Singh @sukritsingh92.bsky.social · Jul 9

On Monday I took my Oath of Allegiance and become a Naturalized US Citizen! Huzzah!

Sukrit, dressed in a blue and gray suit, is standing in front of the stage at a Naturalization ceremony holding a US flag

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Sukrit Singh @sukritsingh92.bsky.social · Jun 28

I was thinking like a 3D Celtic Knot more but pretzel is equally valid (and more delicious)

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Sukrit Singh @sukritsingh92.bsky.social · Jun 28

Can't wait to simulate whatever this is 🤔

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Reposted by Sukrit Singh

Vincent Voelz @voelzlab.bsky.social · Jun 23

Excited to share work now out in #JCIM @acs.org !
doi.org/10.1021/acs....

Alchemical free energy calculations are indispensable in computational drug design. We present an improved approach for optimizing the schedule of alchemical intermediates by minimizing thermodynamic length.

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Simple Method to Optimize the Spacing and Number of Alchemical Intermediates in Expanded Ensemble Free Energy Calculations

Alchemical free energy calculations are essential to modern structure-based drug design. Such calculations are usually performed at a series of discrete intermediates along a nonphysical thermodynamic...

doi.org

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Reposted by Sukrit Singh

Drugs for Neglected Diseases initiative (DNDi) @dndi.org · Mar 25

📢Important announcement! Today, the @asapdiscovery.bsky.social consortium disclosed the structure of our preclinical candidate, ASAP-0017445, a promising broad-spectrum antiviral with potent activity against SARS-CoV2 and other viruses belonging to the same family. (1/10)

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John Chodera @jchodera.bsky.social · Mar 25

This is the moment we've worked toward for a long time: First public disclosure of the @asapdiscovery.bsky.social pan-coronavirus antiviral aiming to help keep humanity safe from future pandemic threats like MERS-CoV and other bat coronaviruses.

Drugs for Neglected Diseases initiative (DNDi) @dndi.org · Mar 25

📢Important announcement! Today, the @asapdiscovery.bsky.social consortium disclosed the structure of our preclinical candidate, ASAP-0017445, a promising broad-spectrum antiviral with potent activity against SARS-CoV2 and other viruses belonging to the same family. (1/10)

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Sukrit Singh @sukritsingh92.bsky.social · Mar 14

Happy Holi, from the @jchodera.bsky.social lab!!

Five people, covered in bright Holi powder, stand arm-in-arm in front of a waterfront railing with a cityscape in the background. They’re all smiling and wearing colorful, powder-stained clothes.

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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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Reposted by Sukrit Singh

C. Brandon Ogbunu @cbo.bsky.social · Mar 6

"No one is coming out of the sky to give you your grant money. Your citation portfolio won’t survive this market crash. Your credentials mean nothing. Everything is going to change."

New for @undark.org

undark.org/2025/03/06/o...

How Science Can Adapt to a New Normal

Opinion | In the wake of attacks on the research enterprise, scientists need to focus on protecting its fragile infrastructure.

undark.org

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Reposted by Sukrit Singh

Prasad Jallepalli, MD, PhD @prasad.bsky.social · Mar 1

NIH operates three cycles of grant review, approval for funding, and actual notice of award

right now all three cycles are blocked

if noncompeting awards are frozen, that's a fourth block

American science is running out of oxygen because of an acute airway obstruction

Zoe McElligott @nanopharmnc.bsky.social · Mar 1

Can speak from personal experience that some non-competitive renewals are also not going out. We were expecting a non-competitive renewal on 2/1/25 that has not been received

Jeremy Berg @jeremymberg.bsky.social · Mar 1

Extending my grant update this morning. Here are data limited to new and competitive renewal applications.

The Pause is dead, Long live the Pause...

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Sukrit Singh @sukritsingh92.bsky.social · Feb 27

It's important to communicate to the public the importance of basic science. Coco is happy to help explain drug binding mechanisms and enzyme kinetics basics:
#scicomm

Composite image illustrating enzyme inhibition concepts with a black dog in different poses:

Top-left: The dog wears a pink flying disc on its head, labeled “Non-competitive (allosteric) inhibition (E–Inc).”
Center: The dog in a tub, tongue out, labeled “E,” connected to “E–S” (enzyme–substrate).
Top-right: The dog holding a yellow tennis ball, labeled “Competitive inhibition (E–Ic).”
Bottom-center: The dog chewing a blue ball, labeled “Substrate binding.” Arrows and labels show the relationships between each form of the enzyme.

Composite image demonstrating “good” versus “bad” enzyme–substrate binding with the same black dog:

Left: The dog with a blue ball in its mouth, labeled “E–Sᵍ” (“bad” binding mode).
Center-left: The dog in a tub with tongue out, labeled “E.”
Center-right: The dog holding a blue ball in a more controlled way, labeled “E–S” (“good” binding mode).
Far right: The dog beside shredded toy pieces, labeled “E + P” (product formation). Text labels and arrows illustrate the transition from enzyme–substrate complexes to products.

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Reposted by Sukrit Singh

Annika Barber @annikabarber.bsky.social · Feb 24

Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...

2025 Study section tracking

docs.google.com

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Reposted by Sukrit Singh

Valerie Horsley @valeriejhorsley.bsky.social · Feb 24

Please share:
@delauro.house.gov is cochair of the US House Congressional Rapid Response Task Force and Litigation Working Group.

They are looking for instances where the impoundment and restriction of NIH/NSF funds is having a negative impact. Submit examples here delauro.house.gov/constituent-...

2025 Federal Financial Assistance Freeze

On Monday, January 27th, 2025, President Trump issued an order to freeze virtually all of approved and legally required federal funding.

delauro.house.gov

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Reposted by Sukrit Singh

Blue Wave 🌊 2028🗽 @jmzmuda.bsky.social · Feb 23

An #NIH-funded research team has developed an mRNA vaccine to treat pancreatic cancer. Results from the clinical trial were published this week in Nature.

#pancreas #cancer #mRNA #vaccine #medsky #science #medicine #bluesky

In Early-Phase Pancreatic Cancer Clinical Trial, Investigational mRNA Vaccine Induces Sustained Immune Activity in Small Patient Group

Learn how MSK researchers are deploying mRNA vaccines against pancreatic cancer.

www.mskcc.org

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Jeremy Berg @jeremymberg.bsky.social · Feb 22

Graduate admissions being put on hold because of the chaos...

Carolyn Ibberson @cbibberson.bsky.social · Feb 22

I created a brief spreadsheet of reductions I've heard of so far. Any additions you know of (especially if you have the links/receipts) would be great: docs.google.com/spreadsheets...

Graduate Reductions Across Biomedical Sciences (2025)

docs.google.com

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Reposted by Sukrit Singh

John Chodera @jchodera.bsky.social · Feb 21

Excited to share what I’ve been working on with @tkaraletsos.bsky.social to transform the field of drug discovery with atomistic foundation simulation models!

I could not be more thrilled to be working with this dream team.

achira.ai

Andrew Dunn @andrewedunn.bsky.social · Feb 21

NEW: Achira has launched with a $33M seed round

I talked with CEO @jchodera.bsky.social about plans to combine AI- and physics-based methods for drug discovery and moving beyond 45 years of the same type of models behind molecular dynamics.

My latest @endpts.com:

endpts.com/achira-raise...

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Reposted by Sukrit Singh

Sonya @sonyahanson.bsky.social · Feb 17

We are hiring a Flatiron Research Fellow in the Structural Molecular Biophysics team! Experience with cryoEM and/or membrane protein simulations are a plus! Happy to chat in person with anyone at #bps2025 ! apply.interfolio.com/160227

Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio

apply.interfolio.com

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Reposted by Sukrit Singh

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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Greg Bowman @drgregbowman.bsky.social · Feb 16

Nice time catching up with folks from @foldingathome.org at #bps2025

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Reposted by Sukrit Singh

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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Sukrit Singh @sukritsingh92.bsky.social · Feb 16

Also from our lab: @markpolk.bsky.social will be presenting a poster (B60, Monday @ 2:45pm) on our high-throughput screening setup that measures kinase-inhibitor binding affinities! Come hear about our robots! bsky.app/profile/mark...

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