Co-founder @Xaira_Thera | @UWProteinDesign PhD instagram.com/definitelyphil
Seattle, WA
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My doctoral advisor @UWMolES / @UWproteindesign (and current scientific advisory board membe @Xaira_Thera) David Baker won the nobel prize!! So stoked and extremely determined to deliver on the promise of this tech! nobelprize.org/prizes/chemis…
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Today in @Nature we compare several compositions of AI-based and classical methods of peptide binder design to make binders to nine different physiologically relevant hormones and cell signaling peptides: nature.com/articles/s41586-0…
Work led with @SusanaVazTor and @PreethamVi
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What an immense privilege to celebrate the #NobelPrize with David, former colleagues from @UWproteindesign , current colleagues at @Xaira_Thera and @RosettaCommons family!
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Online at @ScienceMagazine now: my paper with @FloPraetorius at @UWproteindesign
We made tiny protein hinges that behave similarly to the hinges you encounter in the macroscopic world (gif credit @ichaydon , protein credit yours truly) science.org/doi/full/10.1126…
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While it's still 2022 I want to share some of the cool results in our @biorxivpreprint that we put up recently. (Work with @SusanaVazTor, Isaac Lutz, @PreethamVi, @_JosephWatson, @JosephRog
ers100 and many other incredibly talented individuals) biorxiv.org/content/10.1101/… (1/11)
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It's late but my @biorxivpreprint with @FloPraetorius is out and I'm too excited not to share it with you all #ProteinDesign: biorxiv.org/content/10.1101/…
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Structure-based VHH design preprint is now up! @naterbennett0 @_JosephWatson @RobertRagotte @andrewjborst and special shoutout to @dejsee and Buwei who I collaborated with on this study. Watch this space closely, there's more coming :) @UWproteindesign biorxiv.org/content/10.1101/…
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Super excited to finally see the publication of this great paper in @Nature; this was one of the first projects I got to work on in grad school! Home Depot inspired #ProteinDesign @UWproteindesign Work led by @tim_huddy @kribler Yang and @xu_jinwei
nature.com/articles/s41586-0…
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Moments before realizing I now have to deal with a lifetime of "Dr. Phil" jokes #phdlife #AcademicTwitter
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Awesome paper in @Nature! @ArvindSPillai1 achieved theoretically perfect ligand binding cooperativity with a hill coefficient of ~4 (hemoglobin is ~2.8 by comparison). Congrats Arvind, Abbas, @FloPraetorius and team, truly an honor to help with this work: nature.com/articles/s41586-0…
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5 transformative yrs at @UWMolES @UWproteindesign @datamolecules @uwcse
Much gratitude to everyone, especially advisors David Baker & @jeffnivala
Next: launching a biotech startup with a top-notch team. Stay tuned.
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Preprint is up! Grateful to have co-led this work with @SusanaVazTor , Isaac and @PreethamVi
Thread soon but for now, rest 😂 #AcademicTwitter biorxiv.org/content/10.1101/…
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Excited to finally share what we've been working on since September (but really for over a year)! Great write-up by @AndrewE_Dunn and @RLCscienceboss on Xaira's goal of radically improving the entire drug development pipeline with an AI-first approach endpts.com/in-biggest-ever-b…
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Excited to announce I will be giving a short talk "Multistate Design of Protein Hinge Switches" at #Keystone2023 Computational Design and Modeling of Biomolecules
Hope to see some of you there!
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I believe in #opensource - the whole hinge design pipeline can be found on @github github.com/proleu/hinge_pape…
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📢 We're hiring! On the hunt for a Ph.D. scientist passionate about crafting a state-of-the-art automated wet lab. Dive into protein screening & craft datasets to power our AI in drug discovery. Make a pivotal impact with us. lnkd.in/gBqDvjmh
#BiotechCareers #ProteinDesign
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Love this article by @schubertcm @geekwire on what we're trying to do here in #Seattle at @Xaira_Thera @JustasDauparas @naterbennett0 geekwire.com/2024/inside-the…
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Super excited to see our hinges in action, this was a fun project. Great work @ArvindSPillai1 Abbas and team #ProteinDesign #allostery biorxiv.org/content/10.1101/…
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Thrilled to be a small part of this work. Tune in next time to see the absolutely insane things you can do with MPNN #ItJustWorks #AcademicTwitter
1/5 Robust deep learning based protein sequence design using ProteinMPNN biorxiv.org/content/10.1101/… The high rate of experimental success and applicability to almost any protein sequence design problem has made it the standard approach at the @UWproteindesign github.com/dauparas/ProteinM…
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This is super exciting work - everyone check it out! Grateful for the opportunity to contribute
ProteinMPNN paper: science.org/doi/10.1126/scie…
Github: github.com/dauparas/ProteinM…
Colab notebook: github.com/dauparas/ProteinM…
HuggingFace notebook: huggingface.co/spaces/simond…
Hallucinating symmetric protein assemblies paper:
science.org/doi/10.1126/scie…
Thanks to all collaborators!
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I've been waiting actual years for this tweet
Shoutout to @RavennaBrewing and @Reubensbrews who with their collaborative beer #CrispyShifty unknowingly and retroactively inspired us to design proteins that are both crispy (fully structured and well defined in both states) and shifty (readily switching between both states)
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Separate the military and the police.
The military, supposedly, fights the enemies of the state.
Cops, ostensibly, serve and protect the people.
If your militarize the police, or worse, deploy the military domestically, the enemies of the state tend to become the people.
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Thank you @ShellyFan for this great summary of our work and for including "Flip Flop" in the article (sounds a lot like Phil-ip FloP, which is what @FloPraetorius and I called the hinges for a while) singularityhub.com/2023/08/2… #AI #ProteinDesign
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My lab is trying to make antiviral proteins to help stop Coronavirus and we need your help!
Today we're calling on YOU to help design antiviral proteins against #coronavirus:
fold.it/portal/node/2008926
The most promising solutions will be manufactured & tested at the Institute for Protein Design (@UWproteindesign) in Seattle.
#CitizenScience #COVID #COVID2019 #citsci
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Crispy Shifty concept outlived the beer
Only downer is that @Reubensbrews and @RavennaBrewing are no longer making #crispyshifty, the beer that retroactively inspired us to design proteins that have two fully structured states (=crispy) and readily switch between those states (=shifty).
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Today my pre grad school work with coworkers at @IVinvents and together with @doudna_lab @gavinjknott was published (also my first publication!!): cell.com/iscience/fulltext/S…
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So cool to see #CrispyShifty hinges applied this way! Congrats @adam_broerman
Excited to announce our new #proteindesign strategy for allosterically controlling the kinetics of protein-protein interactions! Read on for cool applications in cytokine signaling, biosensing, and protein circuits. biorxiv.org/content/10.1101/…
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No you're right, we should pay the teacher more
So Biden’s $15 minimum wage comes out to $31,200 a year for a 40 hour work week. The starting salary for a beginning teacher in Texas is $33,660. So a person working a minimum wage job will be making almost the same as a teacher with a college degree. Does this make any sense? 🤷♂️
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We're searching for an expert protein designer to join our Seattle team. If you're passionate about designing molecules to meet unmet medical needs, check this out: linkedin.com/jobs/view/37626…
#ProteinDesign #AI
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Today the New Yorker published a great piece on my lab: newyorker.com/tech/annals-of…
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#CrispyShifty proteins mentioned - highlight of the announcement for me 😁 @ArvindSPillai1 @FloPraetorius
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Tuning the conformational equilibrium with point mutations!! #MultistateDesign win. Absolutely fascinating stuff.
@KortemmeLab
at #KSBiomolecules23
@KeystoneSymp
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common libsolv W ! also parallel downloads and unzipping if you have multiple cores @anacondainc
anaconda.com/blog/conda-is-f…
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Hey Coach Schmelzle, idk if you'll see this but your chem class soph. yr was a major reason why I majored in biochem in undergrad and probably why I'm working on a Molecular engineering PhD now as well. Hope you know you're making a difference.
Today was the first time in my teaching career that I felt defeated by it all, usually I can walk out seeing the glimmer of hope in the next day but today the proverbial mountain is too tall.
Thankfully, tomorrow is a new day...
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Excited to see the future of generative #AntibodyDesign ! Great talk from @PossuHuangLab at #KSBiomolecules23 @KeystoneSymp
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great article on how much progress was made in molecular design and modeling in 2022: cen.acs.org/education/scienc… #proteinMPNN
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At the end of the day, the man who has everything but that which his heart truly desires, often feels as if he has nothing at all. #thought
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Yesterday, myself and others had flash bangs and OC gas fired at us by heavily armed riot cops as we were peacefully protesting. @MayorJenny @SeattleCouncil how long will you allow these uniformed thugs to terrorize us with no accountability? #BlackLivesMatter #HandsUpDontShoot
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Went to a gay nightclub last night on accident. Stayed because all the guys were buying me drinks LOL #theadventuresohPhil
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Proud to announce my commitment to attend the U of M Twin Cities next fall #FutureGopher #skiumah
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had a great time attending #NeurIPS2023 this year! Thanks in particular to the organizers of @workshopmlsb and @genbio_workshop ; cool to see how far things have come just in the last year
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New PI just dropped 👇 great opportunity to get in on the ground floor of a cool lab
Exciting news part 1: I will be joining @ISTAustria as Assistant Professor and will start my own lab for “Biomolecular Design” in March 2024! ista.ac.at/en/research/praet…
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Found out I have a full ride at the U of M yesterday, finished finals today, vaulting at state tomorrow. God is good. #feelingblessed
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IMO the University of Minnesota does not provide adequate support for students who struggle with mental health issues
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Some uplifting news from my lab #SARSCoV2
New: Synthetic proteins designed to bind Spike on SARS-CoV-2 provide starting points for COVID-19 therapeutics. @UWMedicine @veeslerlab @WUSTLmed
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors | science.sciencemag.org/conte…
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Just told my parents I got a minor last weekend while celebrating my birthday and lost all my scholarships #ruthless #AprilFools
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My favorite presentations were @RDasLab with major progress on RNA modeling through crowdsourcing model development, and openreview.net/pdf?id=FhFglO… from @GabriCorso and Arthur Deng et al. showing the importance of valid benchmarks and model accuracy estimators - very critical work
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We also show "in silico" affinity maturation with RFdiffusion: despite high global similarity the glucagon binders before and after partial diffusion exhibit dramatic affinity differences. Xtals show this is due to better contacts with the peptide target #StructuralBiology
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It's a damn shame that this issue only comes to light at the cost of some of the best and brightest among us #MentalHealthAwareness
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Very bold title arxiv.org/abs/2303.12712
Is this the first paper of the #AGI era 😆
Interesting dissection by
@MSFTResearch team
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There, I found the dumbest thing I'll read all week
Millennials are the first gen of women to reject marriage to instead pile up degree upon degree, resulting in debt that, while supposed to help them get established for marriage, instead dealt them a cruel blow: They can't afford to.
@SuzanneVenker
washex.am/2EC8SqN
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Congrats @SusanaVazTor it was an honor to work with you in grad school!
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Huge gratitude to all coauthors especially @SusanaVazTor @PreethamVi , the Joes @_JosephWatson @JosephRogers100 , @mjmaccoss and UW collaborators, all our colleagues at @UWproteindesign , @UWMolES and @jeffnivala , @NSF for funding #ProteinDesign
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According to @fitocracy I lifted 1,968,745 lbs in 2013. Tracking started in May so I definitely went over 2 mil. #stats #wow
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America really be out here failing the tutorial level of the zombie apocalypse game #COVID19
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People who are externally composed and successful are nevertheless quite often experiencing severe mental and emotional distress.
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Also - #AlphaFold can predict conformational changes in designed proteins! We solved crystal structures of my design cs207 matching state X and state YP models I generated with #AF2 . Huge shoutout to the @UWproteindesign cores for this massive #StructuralBiology effort:
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💪💪
Black Lives Matter march going on in Seattle’s International District. More @seattletimes seattletimes.com
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Hey that's me, guess I'm a scientist today
Happening right now: 40 scientists from @UWproteindesign on a video call. We're discussing our new compute capacity, and how to best issue (lots of) new work units.
THANK YOU to all our compute volunteers! We see you, we appreciate you
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emily kicked me in the face on accident and then cried for like 5 minutes while i laughed my butt off haha omg
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Welp looks like I'm an Eagle Scout now... Props to me I guess?! #actuallyprettystoked
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11/10 would do again #KSBioMolecules22 @KeystoneSymp
@KeystoneSymp on computational design of biomolecules was ‼️‼️ Thanks to the organizers for an incredible meeting, full of amazing science, and inviting me to give a short talk.
Sneaking in a few turns ⛷️between sessions wasn't too bad either... 😉
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>> Gopher women's softball team is on the plane
>>> attempts to subtly flirt
>>>> realisation of my severe lack of flirting ability
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Today I bought Valentine's chocolates
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...for my mother #foreveralone
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"Literally all I think about when I eat is, 'is this enough protein?'"
~@emily_gerner ladies and gentlemen
#shesakeeper
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Leadership
Over 4 million on #ClimateStrike today. In 163 countries. And counting...
If you belong to the small number of people who feel threatened by us, then we we have some very bad news for you:
This is just the beginning. Change is coming - like it or not. #FridaysForFuture
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The only thing worse than 8am classes on Fridays is actually trying to go to 8am classes on Fridays
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500 goes out to @Ali_Kat19 @ChristiVetter @parastripathy @NoahKorgs @Preachuk13 @Dexter_Stp @scarlettacts @Owen_Sweeney @evietlarson
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Neat talk from @BShoichet
Docking trillions of small molecules seems computationally challenging - exciting that looks like work being done to quickly summarize sfxn with #GNN and #ActiveLearning
#KSBioMolecules22
@KeystoneSymp
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Abbas and Arvind showed the hinges can be added on to other proteins and used modularly with expected results, as a good hinge should be:
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Ever heard about DALL-E💡? It's an AI that produces images and illustrations that have never existed before. Now, imagine it, but with proteins! @UWproteindesign dropped RFdiffusion: a method for #proteindesign using diffusion models & prediction networks bit.ly/3FXyVsw
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10% luck
20% skill
15% concentrated power of will
5% pleasure
15% pain
100% #reasontorememberthename
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Solid pole vault relay crew @crowley_mason @readreid1 @Nathanmcmillon @Josh_Wagner18 @rileymix46 @StuartHamann2 @kyledillie @LNHS_Track
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Perks of being on crutches: guilt free use of the handicapped stall #crutchislife #rugbyprobs
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'@LNHSWrestling beats South 47-22 in the section quarterfinal @LNHSPanthersAD
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We figured out how to hack #proteinMPNN and used #DeepLearning to solve the multistate sequence design problem - that is, getting a single protein sequence for two different structural states - a significantly more difficult problem than designing for a single structural state
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It's -3 out (-20 for my metric friends). A 5k I didn't train for won't be a problem right? Right? #commitmentday
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