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David Ryan Koes @dkoes.compstruct.org · 17d

Not true - random number generators aren't biased by molecular weight...

Reposted by David Ryan Koes

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 22d

🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.

Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · Aug 19

📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025

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Reposted by David Ryan Koes

Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · Aug 4

Most of MLIPs dont distinguish between spin states, making them unsuitable for open-shell chemistry. We present AIMNet2-NSE (Neural Spin-charge Equilibration), MLIP that incorporates spin-charge equilibration for systems with arbitrary charge and spin. #compchem #skychem
chemrxiv.org/engage/chemr...

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David Ryan Koes @dkoes.compstruct.org · Jul 28

Woohoo!

Gina El Nesr @ginaelnesr.bsky.social · Jul 28

The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬

Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟

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Reposted by David Ryan Koes

Gina El Nesr @ginaelnesr.bsky.social · Mar 20

Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?

@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!

🧵

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David Ryan Koes @dkoes.compstruct.org · Jul 8

Nooooooooo.... 😲

Gina El Nesr @ginaelnesr.bsky.social · Jul 7

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.

Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”

More on the future of MLSB soon…

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Reposted by David Ryan Koes

Sean Eddy @cryptogenomicon.bsky.social · May 22

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

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Reposted by David Ryan Koes

Emma Flynn @emmaflynn.bsky.social · May 27

Our new preprint PharmacoForge: Pharmacophore Generation with Diffusion Models is out now! PharmacoForge quickly generates pharmacophores for a given protein pocket that identify key binding features and find useful compounds in a pharmacophore search. Check it out! 🧪 doi.org/10.26434/che...

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David Ryan Koes @dkoes.compstruct.org · May 19

Was proud and honored to hood Dr. Drew McNutt at the Pitt School of Medicine Diploma Ceremony. Here we are rocking both the blue and gold and tartan colors representing our joint Pitt-CMU CompBio PhD program. Congratulations to Drew and the other @cmupittcompbio.bsky.social graduates!

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Reposted by David Ryan Koes

Dr Javier Sánchez Utgés @javierutges.bsky.social · May 19

I am #exhilarated to share that our new paper "LIGYSIS-web: a resource for the analysis of protein-ligand binding sites" is now published in @narjournal.bsky.social! After almost two years of development and more than 600 commits, LIGYSIS-web is out!

📜 : tinyurl.com/utges-LIGYSI...

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Reposted by David Ryan Koes

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · May 8

Two students in the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology have received honorable mentions from the National Science Foundation’s Graduate Research Fellowship Program. Congratulations to Anamarie Martinez and Emma Flynn!

Read more: tinyurl.com/GRFPPitt

PhD students earn recognition from National Science Foundation fellowship - Department of Computational and Systems Biology

Two students in the Joint Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology have received honorable mentions from the National Science Foundation’s Graduate Research Fellow...

tinyurl.com

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Reposted by David Ryan Koes

Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · Apr 8

We're recruiting a 3-year postdoc for the Novo Nordisk - Oxford Fellowship programme!

Develop machine learning approaches for fragment library design and experimental optimisation

With @fergusimrie.bsky.social and Charlotte Deane

Job advert: shorturl.at/3l47e
Further details: shorturl.at/u4UkK

Job Details

shorturl.at

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David Ryan Koes @dkoes.compstruct.org · Mar 31

Everything is easy in 2D.. - @franknoe.bsky.social

Rishal Aggarwal @rishalchich.bsky.social · Mar 31

New "blogpost" from our lab, that got accepted at ICLR 2025! We compare an old MCMC method known as Sequential Monte Carlo to generative models trained on energy functions (iDEM/iEFM) and show that MCMC does better. Check it out here: rishalaggarwal.github.io/ebmvsmcmc/

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Reposted by David Ryan Koes

Conscience @conscience-network.bsky.social · Mar 25

🚀One week left to register for our Symposium on Open Drug Discovery! Join us in Montreal April 7-8 for an exciting program showcasing how open science and AI are driving drug discovery. Some sessions are already sold out, so register now! Register by April 2nd: conscience.ca/symposium2025

Conscience Symposium on Open Drug Discovery - Submission and registration are open! - Conscience

Registration is now open for the second annual Conscience Symposium on Open Drug Discovery! Join us at the Society for Arts and Technology in Montreal on April 7-8, 2025, for two days of insightful ta...

conscience.ca

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David Ryan Koes @dkoes.compstruct.org · Mar 25

Interested in generative modeling and pharmacophores search for SBDD? Check out our talks at #ACSSpring2025

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Reposted by David Ryan Koes

Alexey Amunts @amunts.bsky.social · Mar 23

www.vant.ai/neo-1

The world's most general-purpose atomistic foundation model, unifying structure prediction and de novo generation for the atoms of life

www.vant.ai

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Reposted by David Ryan Koes

Eric Topol @erictopol.bsky.social · Mar 23

A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved

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Reposted by David Ryan Koes

Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · Mar 18

Our latest ChemRxiv preprint, "Transferable #MachineLearning Interatomic Potential for Pd-Catalyzed Cross-Coupling Reactions" Collaboration with @nsf-ccas.bsky.social @gabegomes.bsky.social @bobbypaton.bsky.social chemrxiv.org/engage/chemr... #compchem #chemsky

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Reposted by David Ryan Koes

Matthieu Schapira @mattschap.bsky.social · Mar 10

The CACHE #2 preprint is now online: bit.ly/3DyCmHN Active learning and fragment growing delivered confirmed hits. A citizen scientist using the Fold-it gaming interface designed the top compound! Kudos to Sasha and Madhushika @thesgc.bsky.social at the bench. @conscience-network.bsky.social

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David Ryan Koes @dkoes.compstruct.org · Mar 7

@standupforscience.bsky.social

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Reposted by David Ryan Koes

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · Feb 17

Andrew McNutt, '24 CPCB graduate, is ready for life's next adventure. Before he begins his career in drug discovery, he's taking a well-deserved break to hike the Appalachian Trail from Georgie to Maine.

Read more: tinyurl.com/AndrewMcNutt

Andrew McNutt on a sola climbing trip in New York

Andrew McNutt poses for a photo with other students in the CPCB program

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Reposted by David Ryan Koes

Stand Up for Science! @standupforscience.bsky.social · Feb 12

Welcome to the Bluesky account for Stand Up for Science 2025!

Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!

#scienceforall #sciencenotsilence

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David Ryan Koes @dkoes.compstruct.org · Feb 8

I’ll have to read the paper, but that’s a bizarre take given the graph. The issue isn’t the amount of data but the ability to generalize from it - which absolutely requires more innovative algorithms.

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Reposted by David Ryan Koes

Razvan Borza @rborza.bsky.social · Nov 5

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔

➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!

🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...

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Reposted by David Ryan Koes

Marco Trizzino @marcotrizzino.bsky.social · Jan 22

NIH council meeting (NIDCR)scheduled for today, where our R01 grant (3rd percentile) was supposed to be discussed, was postponed indefinitely as a consequence of Trump's executive order which ordered pausing of all communications from all federal agencies. Not good.

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