David Ryan Koes
@dkoes.compstruct.org
Removing barriers to computational drug discovery one bit at a time. Associate Professor in Computational and Systems Biology at the University of Pittsburgh.
https://bits.csb.pitt.edu/
https://bits.csb.pitt.edu/
Reposted by David Ryan Koes
🚨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.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025
September 17, 2025 at 2:59 PM
🚨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.
Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
Reposted by David Ryan Koes
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...
chemrxiv.org/engage/chemr...
August 4, 2025 at 4:47 PM
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...
chemrxiv.org/engage/chemr...
Woohoo!
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!🌟
Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
July 28, 2025 at 4:01 PM
Woohoo!
Reposted by David Ryan Koes
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!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
March 20, 2025 at 3:02 PM
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!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
Nooooooooo.... 😲
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…
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…
July 8, 2025 at 10:04 PM
Nooooooooo.... 😲
Reposted by David Ryan Koes
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.
May 22, 2025 at 12:42 PM
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.
Reposted by David Ryan Koes
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...
May 27, 2025 at 7:11 PM
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...
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!
May 19, 2025 at 1:55 PM
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!
Reposted by David Ryan Koes
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...
📜 : tinyurl.com/utges-LIGYSI...
May 19, 2025 at 10:37 AM
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...
📜 : tinyurl.com/utges-LIGYSI...
Reposted by David Ryan Koes
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
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
May 8, 2025 at 3:47 PM
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
Read more: tinyurl.com/GRFPPitt
Reposted by David Ryan Koes
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
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
April 8, 2025 at 3:44 PM
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
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
Everything is easy in 2D.. - @franknoe.bsky.social
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/
March 31, 2025 at 5:03 PM
Everything is easy in 2D.. - @franknoe.bsky.social
Reposted by David Ryan Koes
🚀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
March 25, 2025 at 1:12 PM
🚀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
Interested in generative modeling and pharmacophores search for SBDD? Check out our talks at #ACSSpring2025
March 25, 2025 at 3:15 PM
Interested in generative modeling and pharmacophores search for SBDD? Check out our talks at #ACSSpring2025
Reposted by David Ryan Koes
Reposted by David Ryan Koes
A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved
March 23, 2025 at 4:17 PM
A pie graph worth keeping in mind as the NIH budget plummets jamanetwork.com/journals/jam... for 356 new FDA drugs approved
Reposted by David Ryan Koes
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
March 18, 2025 at 2:12 PM
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
Reposted by David Ryan Koes
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
March 10, 2025 at 9:40 PM
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
March 7, 2025 at 4:56 PM
Reposted by David Ryan Koes
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
Read more: tinyurl.com/AndrewMcNutt
February 17, 2025 at 4:11 PM
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
Read more: tinyurl.com/AndrewMcNutt
Reposted by David Ryan Koes
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
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
February 12, 2025 at 5:04 PM
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
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
Reposted by David Ryan Koes
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...
➡️ 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...
November 5, 2024 at 12:18 AM
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...
➡️ 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...
Reposted by David Ryan Koes
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.
January 22, 2025 at 5:18 PM
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.
Reposted by David Ryan Koes
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...
January 19, 2025 at 4:40 PM
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...
Reposted by David Ryan Koes
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
Follow us for updates about the group's latest work, web app updates, and more.
opig.stats.ox.ac.uk
OPIG
Oxford Protein Informatics Group
opig.stats.ox.ac.uk
January 15, 2025 at 1:53 PM
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
Follow us for updates about the group's latest work, web app updates, and more.
opig.stats.ox.ac.uk