Pascal Sturmfels @PascalSturmfels
PhD student at @uwcse + @UWproteindesign working on machine learning for protein design, protein language models, etc. psturmfels.github.io Seattle, WA Joined December 2019-
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Even though I probably spent more time in the lab playing chess than doing research, for some reason they gave me a PhD 🥳🥳
Even though I probably spent more time in the lab playing chess than doing research, for some reason they gave me a PhD 🥳🥳
That's my designed protein on the cover of Science! Achievement unlocked!
That's my designed protein on the cover of Science! Achievement unlocked!
Researchers in Science present a next-generation protein structure prediction and design tool, #RoseTTAFold All-Atom, that can accept a wide range of ligands and covalent amino acid modifications. Learn more in this week's issue: scim.ag/6Ea
Specifying the input for cofolding models just got easier with my new gradio component "gradio_cofoldinginput". Try it here to generate inputs for RoseTTAfold2 All Atom predictions including covalent modifications: huggingface.co/spaces/simondu…
Specifying the input for cofolding models just got easier with my new gradio component "gradio_cofoldinginput". Try it here to generate inputs for RoseTTAfold2 All Atom predictions including covalent modifications: huggingface.co/spaces/simondu…
Super excited to share our paper “Design of amyloidogenic peptide traps” is out now! 🧠 nature.com/articles/s4158… Special thanks to @eaandrzejewska , Danny Sahtoe and David Baker
We’re excited to share our preprint where we show, for the first time, the atomically accurate design of VHH antibodies!
🧵(1/7) Excited to share that our work, EquiformerV2, has been accepted to #ICLR2024. EquiformerV2 is the state-of-the-art on large-scale atomistic benchmarks -- OC20, OC22, AdsorbML, and ODAC23. Joint work with @bwood_m, @abhshkdz from @OpenCatalyst and @tesssmidt Paper:…
AlphaFold2 and RoseTTAFold are limited to predicting the 3D structure of proteins. A new all-atom method models complete biomolecular assemblies, including proteins, nucleic acids, small molecules, metals, and covalent modifications. #NBThighlight science.org/doi/10.1126/sc…
Our work on modeling and designing biomolecular assemblies is now in @ScienceMagazine. science.org/doi/10.1126/sc… RFAA Code: github.com/baker-laborato… RFdiffusionAA Code: github.com/baker-laborato…
Excited to finally be able to share our ICLR work critically analyzing the capacity of deep learning docking methods to generalize and how to improve this (spoiler scaling, augmentation and RL)! With this, we release a new significantly improved version of DiffDock! A thread! 🧵
Our paper using ProteinMPNN redesign for improved properties is up on JACS! Huge thanks to Reyes, @ikalvet, Sam, and many others for their work. Shout out to @JustasDauparas for developing such a groundbreaking (and versatile!) tool. @UWproteindesign pubs.acs.org/doi/full/10.10…
looking for interns for two projects next summer, come work with me, @nc_frey and the rest of the @PrescientDesign team applying bleeding edge machine learning to fascinating biological data!
looking for interns for two projects next summer, come work with me, @nc_frey and the rest of the @PrescientDesign team applying bleeding edge machine learning to fascinating biological data!
Monday 11am Reading group: RosettaFold all-atom! biorxiv.org/content/10.110… Let us discuss with @r_krishna3 what protein design niceties we can achieve with this. And also the AlphaFold all-atom "glimpse" :) Join on Zoom at 11am ET / 4pm UTC / 5pm CET: portal.valencelabs.com/logg
Soo, this is a big one :) On Nov 20 we will have RosettaFold all-atom in the reading group with @r_krishna3! Quite amazing protein design capabilities. But that is my naive evaluation - join us and let's discuss and hear your insights! Sign up here: portal.valencelabs.com/logg
Thrilled to announce the opening of the Srivatsan Lab (srivatsan-lab.com) at the @fredhutch. The lab will be building new sequencing technologies to understand how our cells and bodies form over the course of development.
Thrilled to announce the opening of the Srivatsan Lab (srivatsan-lab.com) at the @fredhutch. The lab will be building new sequencing technologies to understand how our cells and bodies form over the course of development.
RFdiffusionAA generating a small molecule binding protein against an experimental FXIa inhibitor (OQO), a ligand which is significantly different than any in its training dataset.
RFdiffusionAA generating a small molecule binding protein against an experimental FXIa inhibitor (OQO), a ligand which is significantly different than any in its training dataset. https://t.co/JyHKu2Jylf
RoseTTAFold updated to be All-Atom... biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications ... and diffusion🤯biorxiv.org/content/10.110…
All-atom version of RoseTTAFold looks quite exciting! biorxiv.org/content/10.110…
We made RoseTTAFold that predicts everything in the PDB, not just proteins, the used it to make RFDiffusion that generates ligand-binding proteins, including a 10nM binder of digoxigenin. See @r_krishna3's thread for details.
We made RoseTTAFold that predicts everything in the PDB, not just proteins, the used it to make RFDiffusion that generates ligand-binding proteins, including a 10nM binder of digoxigenin. See @r_krishna3's thread for details.
Very excited to share RoseTTAFold All-Atom and RFdiffusion All-Atom, methods for structure prediction and design of biomolecular assemblies! biorxiv.org/content/10.110… 1/n
Sergey Ovchinnikov @sokrypton
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David Juergens @DaveJuergens
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Ellen Zhong @ZhongingAlong
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Jue Wang @jueseph
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Lior Pachter @lpachter
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Jinwoo Leem @ideasbyjin
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Saacnicteh Toledo-Pat... @SaacNicteh
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Jose Bustamante S (he... @jos3bustamant3
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Pat Erickson 🧪⚗�... @ShamokinChemist
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Mark Neumann @MarkNeumannnn
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Chris Myers 💻🧬�... @bayouphysicist
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Gulam Sarwar Chuwdhur... @GSChuwdhury
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Premraj Thakur @PremrajThakur8
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Ruidong Wu @RuidongWu
213 Followers 531 Following PhD student at @MIT_CSAIL. Prev: @HelixonBio @UofIllinois @Tsinghua_Uni.
Michael Bronstein @mmbronstein
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Kristian Frandsen �... @KrFrandsen
967 Followers 4K Following Researcher @DTUbioengineer Enzyme Discovery | Guest researcher @cpsc_ucph @KU_PLEN | former @HOPE_NNF and #INRAE @BBF_lab | #CAZymes #cryoEM #Engineering #AI
Chirag Lakhani @cmlakhan
563 Followers 4K Following Currently: Staff Scientist @nygenome in the @david_a_knowles lab. Previously: @HarvardDBMI Postdoctoral Research Fellow in @chiragjp lab https://t.co/APTLHsivM2
Hudson Kalmans @HKalmans
75 Followers 996 Following BAKER LAB @UWproteindesign IT DOESNT GET BETTER THAN THIS
Varela @dvarelaTW
210 Followers 3K Following protein design, art, python, jokes, artificial intelligence, cinema... you can really expect everything here. (Spanish/English)
Chase Armer @ChaseArmer
229 Followers 461 Following PhD @ Columbia University | 2x Synbio Founder | Protein Engineering Tournament | Combining AI with cloud labs to build self-driving systems for science
Rajan Kumar Kharwar @rajanKumarkhar8
728 Followers 6K Following PhD Candidate @GroupMarek | Schulich Faculty of Chemistry | Technion
Theo Jalabert @theo_jala
171 Followers 272 Following product engineer @adaptyvbio - building software for protein design
Xiaoya Li @xxiaoyali_
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Davian Ho @iceindavain
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Mike Ge @mikefzge
246 Followers 366 Following PGY-4 @UofTanesthesia, MD '22 @McMasterU, and BSc '19 @westernuBiochem.
Alireza Hashemi @AlirezaHasheml
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lili @lili04990164
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sarrah @AgaRosegirl
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Sergey Ovchinnikov @sokrypton
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Kevin K. Yang 楊凱�... @KevinKaichuang
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David Juergens @DaveJuergens
3K Followers 2K Following Machine learning for molecular design. Currently: Postdoc @StanfordUChem @mtzlab. PhD @UWMolES @UWproteindesign. B.S. @UWChemE
Anshul Kundaje (anshu... @anshulkundaje
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Noelia Ferruz @ferruz_noelia
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Alex Rives @alexrives
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Stephen Ra @stephenrra
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Ellen Zhong @ZhongingAlong
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Jue Wang @jueseph
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246 Followers 366 Following PGY-4 @UofTanesthesia, MD '22 @McMasterU, and BSc '19 @westernuBiochem.
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Alex Morehead (何聪... @MoreheadAlex
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Andrew Hunt @Andrew_C_Hunt
345 Followers 444 Following #protein enthusiast and #cellfree evangelist | @newmexicotech to @nu_chbe to @UWproteindesign | Team lead EBRC In Translation Podcast
Ian Haydon @ichaydon
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524 Followers 2K Following Now a quantitative researcher at a hedge fund. Previously worked in computational biology & bioinformatics.
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Leo Zang @LeoTZ03
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Chris Lin @chrislin97
69 Followers 65 Following PhD student @uwcse. Previously @ucberkeley and @stanford.
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Nathan C. Frey @nc_frey
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Shunzhi Wang @wang_shunzhi
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Florian Praetorius @FloPraetorius
688 Followers 207 Following Biomolecular designer; currently postdoc @UWproteindesign; starting my lab @ISTAustria in March 2024 @flopraetorius.bsky.social
Linna An @alchemist_an
764 Followers 471 Following TTAP @RiceUniversity | computational biochemist | Protein designer @UWproteindesign & natural product biochemist @ChemistryUIUC | open to industry
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Ben Chamberlain @DrBPChamberlain
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Demis Hassabis @demishassabis
488K Followers 146 Following Nobel Laureate. Co-Founder & CEO @GoogleDeepMind - working on AGI. Solving disease @IsomorphicLabs. Trying to understand the fundamental nature of reality.
Tim Green @tfgg2
3K Followers 2K Following Research Engineer at @GoogleDeepMind, co-led the AlphaFold team, now working on LLMs for science. Previously @democlub and physics.
Benedikt Singer @SingerBenedikt
82 Followers 199 Following PhD Student at EPFL, Switzerland | Working on AI for Protein Design | he/him | Find me on BlueSky: @benediktsinger.bsky.social
Michael Albergo @msalbergo
2K Followers 2K Following Junior fellow at the Society of Fellows at @Harvard and @iaifi_news fellow, incoming Assistant Professor at @Harvard and the @KempnerInst views my own
Hannes Stärk @HannesStaerk
12K Followers 407 Following @MIT PhD student • ML for molecules and biology https://t.co/hEtGZrEHqu
Jason Yim @json_yim
2K Followers 323 Following PhD student @MIT_CSAIL. Generative models, protein design. 🦋 Bluesky handle: https://t.co/MPlEjog02q On X until the exodus is complete.
Alex Chu @alexechu_
2K Followers 749 Following Deep learning & protein design. @googledeepmind PhD @Stanford
Una Wen-lii Natterman... @unattermann
867 Followers 869 Following she/her | Co-Founder & Scientist @Pioneer__Labs | Formerly: Postdoc @MITdeptofBE Voigt Lab 🧬🧫 PhD @UWproteindesign 💎🔬
Indrek Kalvet @ikalvet
658 Followers 334 Following 🇪🇪 De Novo enzyme design • HHMI Postdoc at the Institute for Protein Design at University of Washington @UWproteindesign
Andy Hitchcock @HitchcockLab
277 Followers 246 Following Royal Society University Research Fellow at the University of Sheffield
Kiera Sumida @KieraSumida
367 Followers 78 Following Enzyme designer // PhD student @UWproteindesign
Bruno Correia @befcorreia
3K Followers 735 Following Professor in Bioengineering @epfl 🇨🇭| protein designer
Helen Eisenach O'Brie... @HelenEisenach
858 Followers 324 Following Baker & King labs @UWproteindesign | alum @Harvard | novel protein nanomaterials and deep learning
Thomas Schlichthaerle @schlichthaerle
491 Followers 385 Following PostDoc working on Protein Design problems in the Baker Lab, previously working with DNA-PAINT & DNA Nanotechnology
Boston Protein Design... @ProteinBoston
5K Followers 76 Following a community of computational protein engineers and modelers from both academia and industry an @openmsf project organized by @bahl_lab @nickpolizzi_ @sokrypton
Green Ahn @Green_Ahn
637 Followers 210 Following @JCChildsFund Postdoctoral Fellow in David Baker’s Lab at IPD @UWproteindesign. PhD w/ @CarolynBertozzi @Stanford
Oxford Protein Inform... @OPIGlets
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