MLSB (in San Diego + Copenhagen)

24 Nov 2025

🧬 Attending EurIPS in Copenhagen? Come join us for ML×SBio Drinks! Join CradleBio & @adaptyv.bio for an evening of conversation at the intersection of machine learning and structural biology. 📍 Copenhagen | EurIPS week 🎟️ Space limited—RSVP to secure your spot

luma.comMLSB @ EurIPS Happy Hour: Cradle x Adaptyv · LumaBrought to you by Machine Learning in Structural Biology (MLSB) at EurIPS 2025! Join Cradle and Adaptyv Bio for drinks and conversation at the intersection of…

24 Nov 2025

Hosted by EurIPS MLSB workshop organizers. RSVP below ⬇️ luma.com/e0avnsib

jonathanziegler.bsky.social

25 Sept 2025

Reminder that MLSB submissions for ✨BOTH✨ the Copenhagen and the San Diego MLSBs are due one week from now on October 1st 11:59pm AoE!

MLSB (in San Diego + Copenhagen) reposted

@jonathanziegler.bsky.social

18 Sept 2025

EuroMLSB at EurIPS is confirmed and the submission deadline is set to Oct 1st. This is **earlier than the EurIPS-suggested workshop deadline** for a reason: we have a shared submission process with MLSB in SanDiego for which the deadline is now also extended to Oct 1st!

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

🚨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.

17 Sept 2025

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

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

12 Sept 2025

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉 Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

12 Sept 2025

Submissions will use the same system, and all papers—regardless of location preference—will receive the same level of review and be evaluated under identical acceptance criteria.

12 Sept 2025

More information about speaker lineup coming soon 😎 None of this would have been possible without @patrickkidger.bsky.social and @jonathanziegler.bsky.social 🙌

19 Aug 2025

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

mlsb.ioMLSB 2025 WorkshopWorkshop on Machine Learning in Structural Biology co-located with NeurIPS 2025

19 Aug 2025

Information on submission guidelines are on our website at mlsb.io/call-for-papers Specifically, we ask all authors to adhere to the NeurIPS Rules on use of LLMs!

28 July 2025

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

Gina El Nesr@ginaelnesr.bsky.social

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!🌟

MLSB (in San Diego + Copenhagen) reposted

Gina El Nesr

@ginaelnesr.bsky.social

7 July 2025

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…

Interested in turning your workshop paper into a publication? MLSB has partnered with PRX Life to start a new special collection! Submission is free and open access - Editorial: tinyurl.com/mlsbeditorial Collection: go.aps.org/4fWvbHe Submission: go.aps.org/3Znaux5

Brought to you by @ginaelnesr.bsky.social @gcorso.bsky.social @hkws.bsky.social @sesamedusa.bsky.social

docs.google.comMLSB Post-Conference SurveyThank you for taking a few minutes to complete this survey about your experience at MLSB 2024 @ NeurIPS! Your feedback is valuable and ensures that we run a smooth workshop each year.

Thank you to everyone who came to MLSB this year!! We are collecting feedback in a short 2 minute survey (and more data means maybe next year we'll train a new model... or just get a bigger room 😄) forms.gle/WHFNfvxVh3Qx...

Equally, big thank you to our sponsors whom without would not have made MLSB possible. If you or your team is interested in sponsoring MLSB next year, please reach out!

Next up we're highlighting the results of the PINDER and PLINDER challenge.

View full thread

pinder.shPINDER: Unlocking new discoveries through a scale-shift in data and real-world relevant and rigorous evaluationsPINDER is an academic-industry collaboration offering a gold standard dataset and evaluations for computational protein-protein interactions prediction.

PINDER: pinder.sh PLINDER: plinder.sh

huggingface.coLeaderboard2024 - a Hugging Face Space by MLSBDiscover amazing ML apps made by the community

Leaderboard is graciously hosted by HuggingFace here: huggingface.co/spaces/MLSB/...

Time for the MLSB Panel 🎛️ We're welcoming @grocklin.bsky.social @noeliaferruz.bsky.social Erika Alden DeBenedictis @milot.bsky.social Jennifer Listgarten to the panel, hosted by the wonderful @hkws.bsky.social . 🔥

Next up we're highlighting the results of the PINDER and PLINDER challenge.

Next up - contributed talk. HelixFlow, SE(3)–equivariant Full-atom Design of Peptides With Flow-matching Models Xuezhi Xie, Pedro A Valiente, Jisun Kim, Jin Sub Lee, Philip Kim

Check out the paper here: www.mlsb.io/papers_2024/...

mlsb.iomlsb.io

Next up, contributed talk! FlowPacker: protein side-chain packing with torsional flow matching Jin Sub Lee, Philip Kim

biorxiv.orgFlowPacker: Protein side-chain packing with torsional flow matchingAccurate prediction of protein side-chain conformations is necessary to understand protein folding, proteinprotein interactions and facilitate de novo protein design. Here we apply torsional flow matc...

Check out the paper: www.biorxiv.org/content/10.1...

Next up - invited speaker! Boltz-1: Democratizing Biomolecular Interaction Modeling @jeremywohlwend.bsky.social

Please check out the paper here: www.biorxiv.org/content/10.1...

biorxiv.orgbiorxiv.org

Next up, invited speaker! Challenges to metagenomic annotation with Foldseek and protein language models @milot.bsky.social

View full thread

github.comRelease MMseqs2 Release 16-747c6 · soedinglab/MMseqs2MMseqs2 Release 16 introduces support for GPU-accelerated searches [1]. Additionally, we fixed numerous bugs and relicensed MMseqs2 under the MIT license. [1] Kallenborn F, Chacon A, Hundt C, Sirel...

Check out the amazing codebase for MMseqs2-GPU here. github.com/soedinglab/M...

search.foldseek.comFoldseek Search ServerFoldseek Server offers fast and sensitive protein structure alignments against large protein structure collections

And the Foldseek webserver can be found here: search.foldseek.com/search

Next up, invited speaker! Challenges to metagenomic annotation with Foldseek and protein language models @milot.bsky.social

Next up - Contributed Talk Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference Shayan Shekarforoush @davelindell.bsky.social @marcusabrubaker.bsky.social David Fleet

arxiv.orgCryoSPIN: Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose InferenceCryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The com...

Check out the paper here: arxiv.org/abs/2406.10455

Next up - Contributed Talk! Generative modeling of protein ensembles guided by crystallographic electron densities Sai Advaith Maddipatla · Nadav Sellam · @sankethvedula.bsky.social · Ailie Marx · Alex Bronstein

Check out the paper here: www.mlsb.io/papers_2024/...

mlsb.iomlsb.io