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David Ryan Koes

@dkoes.compstruct.org
1.2K followers 760 following 84 posts

Removing barriers to computational drug discovery one bit at a time. Associate Professor in Computational and Systems Biology at the University of Pittsburgh. bits.csb.pitt.edu

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David Ryan Koes @dkoes.compstruct.org · 09/12/2025
Had an informative and enjoyable time at NeurIPS and MLSB. It was great to see my students present their work and catch up with other CPCB students, both past and present.
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David Ryan Koes @dkoes.compstruct.org · 07/12/2025
Excited to be at the first independent @workshopmlsb.bsky.social
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David Ryan Koes @dkoes.compstruct.org · 05/12/2025
If you like to sample from the Boltzmann distribution and are in San Diego for NeurIPS, be sure to check out Rishal's (@rishalchich.bsky.social) poster (#2110). Great work with Nick Boffi (@nmboffi.bsky.social) and Jacky Chen. neurips.cc/virtual/2025... arxiv.org/abs/2507.00846
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 17/09/2025
🚨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.
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Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 04/08/2025
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 · 28/07/2025
Woohoo!
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Gina El Nesr @ginaelnesr.bsky.social · 20/03/2025
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 · 08/07/2025
Nooooooooo.... 😲
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Emma Flynn @emmaflynn.bsky.social · 27/05/2025
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 · 19/05/2025
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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Dr Javier Sánchez Utgés @javierutges.bsky.social · 19/05/2025
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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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 08/05/2025
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
tinyurl.com
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...
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Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · 08/04/2025
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
shorturl.at
Job Details
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David Ryan Koes @dkoes.compstruct.org · 31/03/2025
Everything is easy in 2D.. - @franknoe.bsky.social
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Conscience @conscience-network.bsky.social · 25/03/2025
🚀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.ca
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...
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David Ryan Koes @dkoes.compstruct.org · 25/03/2025
Interested in generative modeling and pharmacophores search for SBDD? Check out our talks at #ACSSpring2025
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Alexey Amunts @amunts.bsky.social · 23/03/2025
www.vant.ai/neo-1
vant.ai
The world's most general-purpose atomistic foundation model, unifying structure prediction and de novo generation for the atoms of life
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Eric Topol @erictopol.bsky.social · 23/03/2025
A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved
graph of NIH basisfor new drugs
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Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 18/03/2025
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
Transferable MachineLearning Interatomic Potential for Pd-Catalyzed Cross-Coupling Reactions
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Matthieu Schapira @mattschap.bsky.social · 10/03/2025
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 · 07/03/2025
@standupforscience.bsky.social
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Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 17/02/2025
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 YorkAndrew McNutt poses for a photo with other students in the CPCB program
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Stand Up for Science! @standupforscience.net · 12/02/2025
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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Razvan Borza @rborza.bsky.social · 05/11/2024
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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Marco Trizzino @marcotrizzino.bsky.social · 22/01/2025
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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Diego del Alamo @delalamo.xyz · 19/01/2025
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
Protein structure embeddings reveal undersampled and de novo structure space. (B) First two principal components of mean-pooled ESM3 embeddings colored by helix content determined by DSSP. The indicated dashed guide lines denote visual boundaries of native structure space not sampled (Undersampled) and novel regions of protein structure for this space only observed in samples but not in native structures (De novo). (C) Rasterized visualization of panel B with 16 equally spaced grid squares in each principal component axis. A representative structure from each grid was chosen at random. Empty grid squares indicate the absence of any structure in the enclosed region. De novo alpha helices are shaded along the lower-right diagonal and the structures from CATH which do not have corresponding structures in the samples are shaded along the left and top rims. The structures are displayed in CATH raster plot are given in the Supplementary Information.
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Oxford Protein Informatics Group (OPIG) @opig.stats.ox.ac.uk · 15/01/2025
OPIG is now on Bluesky! Follow us for updates about the group's latest work, web app updates, and more. opig.stats.ox.ac.uk
opig.stats.ox.ac.uk
OPIG
Oxford Protein Informatics Group
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Frank Noe @franknoe.bsky.social · 13/01/2025
If you want to learn more about BioEmu, join Sarah Lewis and Michael Gastegger in @hannes-stark.bsky.social ‘s online seminar today. bsky.app/profile/hann...
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David Ryan Koes @dkoes.compstruct.org · 03/01/2025
Rishal’s colab notebook will suggest pharmacophores given a receptor structure that can be directly imported into Pharmit for screening. Check it out!
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Geoff Hutchison @geoffhutchison.net · 30/12/2024
I wrote up a 2024 Year in Review for @avogadro.cc 🧪⚗️ #opensource #chemsky In short, the community is amazing. Significant translations into 17 languages including 🇭🇷🇫🇷🇭🇺🇰🇷🇷🇴🇪🇸Tamil, 🇺🇦🇨🇳🇬🇪🇩🇪🇯🇵🇵🇹🇧🇷🇷🇸🇹🇷 .. and of course dozens of features and bug fixes discuss.avogadro.cc/t/2024-year-...
discuss.avogadro.cc
2024 Year-In-Review
While it’s not strictly the end of 2024, I wanted to draft this early. Obviously a highlight is the release of 1.99 in time for Ubuntu LTS (24.04) … a summer of great coding / rendering, leading to t...
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David Ryan Koes @dkoes.compstruct.org · 24/12/2024
These ligands make up 33% of the v2 plinder test set (shown with counts): MG 94 NAG 72 NAG-NAG 64 ZN 44 MN 32 BMP 30 HEM 24 EDO 18 SO4 17 PO4 16 ADP 15 GOL 13 ANP 13 CA 13 FMN 11
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Janani Durairaj (Jay) @ninjani.bsky.social · 24/12/2024
Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving. Happy holidays everyone! www.plinder.sh/blog/updates
plinder.sh
Updates
Updates
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Gabriele Corso @gcorso.bsky.social · 21/12/2024
Boltz v0.4.0 is here! Today, we’re releasing our full data processing pipeline, making it easier than ever to build on top of Boltz. This release also includes our evaluation code and new results. Oh, and also pocket conditioning :)
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Lena Steckelberg @lenasteckelberg.bsky.social · 20/12/2024
Hi Bluesky, just in time for the holidays I am excited to share the latest pre-print from my group! We solved the 3D structure of a mysterious viral RNA that resists degradation by host nucleases. A short 🧵 &link below – please also check out the full video! #RNA #RNAbiology #RNASky #lovevirology
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CPCB @cmupittcompbio.bsky.social · 19/12/2024
Last week several of our students presented their research at NeurIPS 2024 in Vancouver. We are so proud of the excellent work that they've accomplished and shared with the scientific community! 🧪 Check out each of their papers below:
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Alexey Amunts @amunts.bsky.social · 07/12/2024
New version of Dockformer preprint landed on arXiv. This virtual screening docking method outperforms all Deep Learning-based approaches, achieving success rates of 90.53% on PDBbind and 82.71% on PoseBusters. Expected to accelerate drug discovery and reduce drug design costs.
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Cas @caswognum.nl · 17/12/2024
With @polarishub.io we’ve built out infrastructure to make hosting and using large scale, ML ready dataset and benchmarks easy. In addition to the dataloaders, we could also maintain leaderboards. Would be happy to explore ways in which we can support the awesome work you’re doing with Plinder.
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 16/12/2024
The American Journal of Human Genetics sat with @fritzroth.bsky.social in the latest "Inside AJHG" to discuss his recently published paper, “A missense variant effect map for the human tumor suppressor protein CHK2.”➡️https://www.ashg.org/ajhg/inside-ajhg-with-fritz-roth/ #ASHG #GeneticsDiscoveries
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Ian Dunn @ian-dunn.bsky.social · 11/12/2024
I'm presenting a new paper "Exploring Discrete Flow Matching for 3D De Novo Molecule Generation" at @workshopmlsb.bsky.social this week! More info in this thread but reach out if want to chat at NeurIPS about generative models or molecular design. arxiv.org/abs/2411.16644
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David Ryan Koes @dkoes.compstruct.org · 15/12/2024
Going into @workshopmlsb.bsky.social , a few thoughts on the PLINDER dataset. This is a monumental and highly appreciated undertaking for extracting protein-ligand interactions from the PDB. First the good...
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David Ryan Koes @dkoes.compstruct.org · 15/12/2024
@workshopmlsb.bsky.social
Huge turnout for MLSB
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Leo Zang @leozang.bsky.social · 14/12/2024
Concept Bottleneck Language Models For protein design - Introduce CB-pLM (Concept Bottleneck Protein Language Models) from 24M to 3B, trained on UniRef50 and SwissProt over 718 concepts (including Cluster name, Biological process, and Biopython-derived features, etc.) arxiv.org/abs/2411.06090
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David Ryan Koes @dkoes.compstruct.org · 15/12/2024
It’s worth opening the notebook if only to see the cool molecular animations in py3dmol.
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Ian Dunn @ian-dunn.bsky.social · 15/12/2024
FlowMol at your fingertips! We just released a colab notebook to make using FlowMol super easy. Come chat with us tomorrow at @workshopmlsb ! #NeurIPS2024 🧪 colab.research.google.com/github/Dunni...
colab.research.google.com
Google Colab
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Marc Lensink @marclensink.bsky.social · 12/12/2024
Early December, the CASP16 Meeting was held in the Palladium resort in Punta Cana, Dominican Republic. Nick Grishin, myself, and Qian Qong presented the assessment of the monomeric structure predictions, the assembly predictions and of monomers in their oligomeric context. 1/n
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Frank Noe @franknoe.bsky.social · 11/12/2024
Excited about BioEmu? Opening this position for just a few days over #NeurIPS2024. Looking especially for Bioinformatics + Structural Biology skills, MD/Stat Mech skills and/or #deeplearning architecture design + engineering skills aka.ms/ai4science-r...
aka.ms
Search Jobs | Microsoft Careers
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David Ryan Koes @dkoes.compstruct.org · 11/12/2024
More excellent work from the indomitable @ian-dunn.bsky.social Come check it out at @workshopmlsb.bsky.social
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David Ryan Koes @dkoes.compstruct.org · 10/12/2024
CACHE3 results are out. We didn’t participate because I didn’t have my act together, but it looks like a win for deep docking. When will nextgen end-to-end DL docking show up/take over in these super important exercises? @conscience-network.bsky.social cache-challenge.org/results-cach...
cache-challenge.org
Results of Cache Challenge # 3 | CACHE
Accelerating the impact of AI-driven Drug Discovery
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