iiinova — where your digital self keeps evolving

Sukrit Singh @sukritsingh92.bsky.social · 08/10/2026

📣 This work is now out in J. Med. Chem.! 📣 "How many crystal structures do you need to trust your docking results?" Link: doi.org/10.1021/acs.... We identify a point of diminishing returns with pose-prediction as you add more experimental reference structures into your docking pipeline!

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Sukrit Singh @sukritsingh92.bsky.social · 02/10/2026

+1 to Hugo! It's a great static site generator and the themes are plentiful and very nice!

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Sukrit Singh @sukritsingh92.bsky.social · 23/09/2026

📣 New preprint 🧪 Physical priors improve performance of structure-based binding affinity models Mtenn decomposes binding affinity prediction into Representation, Strategy, and Readout. E(3)-invariance & splitting components into separate embeddings improves performance! doi.org/10.64898/202...

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Sukrit Singh @sukritsingh92.bsky.social · 15/09/2026

📣 The Singh Lab opens at Fox Chase Cancer Center in Spring 2027, where I will be starting as an Assistant Professor!📣 Excited to continue studying how protein biophysics shapes drug response. I am hiring across all levels and disciplines! Apply on the "Join" page ( & spread the word!): singhlab.bio

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Sukrit Singh @sukritsingh92.bsky.social · 03/08/2026

📣 ❗2nd Preprint of the Summer ❗ 📣 "Kinase inhibitors can change protonation or tautomeric state upon binding." LInk: doi.org/10.64898/202... We find that kinase-inhibitors can change in net-charge and tautomer state upon binding (from solution-state to kinase-bound), affecting med-chem choices!

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Jeremy Berg @jeremymberg.bsky.social · 24/07/2026

SO if they want to experiment with how science is conducted in the United States, they should make substantial donations to a foundation that would open up transparent competitions for funding, in partnership with federal agencies (with minimal strings attached other than process-related ones). 3/5

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Sukrit Singh @sukritsingh92.bsky.social · 08/07/2026

Shout out to @ppxasjsm.bsky.social, @matteodegiacomi.bsky.social, and Ryan Zhu for their efforts! And a big thank you to @foldingathome.org donors for their compute contributions that made this study possible!

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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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Sukrit Singh @sukritsingh92.bsky.social · 23/06/2026

Now out in the Special Issue on "New Concepts in Drug Discovery: Drug residence time!" Edited by Markus Seeliger & Ruth Nussinov, the reviews cover new computational and experimental methodologies for predicting ligand affinity & kinetics. Link: www.sciencedirect.com/special-issu...

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Don Moynihan @donmoyn.bsky.social · 01/06/2026

A proposed Trump policy would put Russ Vought in charge of American science. Its an example of the slow creep of politicization into processes that both parties traditionally understood as needing nonpartisan and expert guidance. What can you do about it? 🧵 donmoynihan.substack.com/p/the-creep-...

donmoynihan.substack.com

The Creep of Politicization

A new assault on science highlights a broader pattern

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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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Sukrit Singh @sukritsingh92.bsky.social · 13/03/2026

"Reject doomscrolling. Embrace naptime"

A dark brown dog with a graying muzzle stands on a couch, facing the camera with wide, shiny eyes and its tongue playfully sticking out. The dog wears a collar with tags, and a pink blanket is draped beside it. Soft daylight from a nearby window illuminates the cozy indoor scene.

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Katie Langin @klangin.bsky.social · 26/01/2026

How many STEM Ph.D.s were lost from the U.S. federal government last year? My colleagues @mghersher.bsky.social and @policyhound.bsky.social dug into a recent data release to find the answer. A @science.org exclusive. www.science.org/content/arti...

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Dr Kathleen Millen @neurodevkathy.bsky.social · 02/01/2026

I don't think you non-science people realize what it takes to get a grant funded by NIH. Started experiments in Sept 2021 to generate 3 new mouse mutants to model human disease. Prelim dara shows they have relevant disease phenotypes worthy of study. Need a small grant first to characterize /1

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John Chodera @jchodera.bsky.social · 27/12/2025

This is more than half the NSF's total annual budget.

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Sukrit Singh @sukritsingh92.bsky.social · 12/12/2025

New preprint! How many crystal structures do you need to trust your docking results? It turns out, if you know how your main scaffold binds in the pocket, not that many! Check out this work from recently-defended lab member @keysandcompounds.bsky.social On BioRxiv: www.biorxiv.org/content/10.1...

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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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Dr. Fiona @fionachembot.bsky.social · 17/11/2025

Are you a postdoc stuck in the US?! Is your research stalled or are you in any way affected by the whims of that unfettered madman? Interested in MD simulations of large biomolecules?! Consider joining me at the University of Freiburg! uni-freiburg.de/frias/call-f...

uni-freiburg.de

Call for Applications: Early Career Rescue Fellowship – Freiburg Institute for Advanced Studies

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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/09/2025

How many crystal structures do you need to trust your docking results? www.biorxiv.org/content/10.1101/202…

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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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Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · 15/09/2025

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

mskcc.org

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?

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Sukrit Singh @sukritsingh92.bsky.social · 09/07/2025

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 · 28/06/2025

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 · 28/06/2025

Can't wait to simulate whatever this is 🤔

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Vincent Voelz @voelzlab.bsky.social · 23/06/2025

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. 1/7

doi.org

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...

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Drugs for Neglected Diseases initiative (DNDi) @dndi.org · 25/03/2025

📢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 · 25/03/2025

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.

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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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C. Brandon Ogbunu @cbo.bsky.social · 06/03/2025

"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...

undark.org

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.

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Prasad Jallepalli, MD, PhD @prasad.bsky.social · 01/03/2025

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

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Sukrit Singh @sukritsingh92.bsky.social · 27/02/2025

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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Annika Barber @annikabarber.bsky.social · 24/02/2025

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...

docs.google.com

2025 Study section tracking

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Valerie Horsley @valeriejhorsley.bsky.social · 24/02/2025

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-...

delauro.house.gov

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.

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Jeremy Berg @jeremymberg.bsky.social · 22/02/2025

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

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John Chodera @jchodera.bsky.social · 21/02/2025

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

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Sonya @sonyahanson.bsky.social · 17/02/2025

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.com

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

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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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Greg Bowman @drgregbowman.bsky.social · 16/02/2025

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

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

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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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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Tori Barber @vbarber.bsky.social · 28/01/2025

**screams in early career scientist**

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Claus Wilke @clauswilke.com · 17/12/2024

Bioart, courtesy of the NIH. All images are in the public domain and available for download as high-quality SVGs. bioart.niaid.nih.gov

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Sukrit Singh @sukritsingh92.bsky.social · 09/12/2024

Excellent winter vacation vibes: A book on the Science of Indian cooking (from Krish Ashok) paired with an amazing coconut-washed Old Fashioned from Dishoom.

A view of an indoor lounge in the restaurant Dishoom in London. In the middle is a coffee table which has a cocktail and a book. The cocktail is an Old Fashioned that came in a bottle and a separate glass of ice to pour small amounts into. The book is Masala Lab from Krish Ashok on the Science of Indian cooking

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Sukrit Singh @sukritsingh92.bsky.social · 03/12/2024

Nothing to be sorry for! We're trying to scale up an elegant turn-on fluorescence readout that some FDA-approved kinase inhibitors are capable of (journals.plos.org/plosone/arti...) - we're trying as many kinase-inhibitor pairs as we can to generate an initial dataset of binding measurements!

journals.plos.org

Structural and Spectroscopic Analysis of the Kinase Inhibitor Bosutinib and an Isomer of Bosutinib Binding to the Abl Tyrosine Kinase Domain

Chronic myeloid leukemia (CML) is caused by the kinase activity of the BCR-Abl fusion protein. The Abl inhibitors imatinib, nilotinib and dasatinib are currently used to treat CML, but resistance to t...

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