Daniel Keedy
@dkeedy.bsky.social
PI of the #keedylab at the CUNY Advanced Science Research Center & City College of New York. Interests: protein structural biophysics & puns. https://keedylab.org
Props to my colleague here at the @asrc-gc.bsky.social , @fravallese.bsky.social , for this wonderful piece about the uniquely strong structural biology community here in NYC. I often feel lucky to be here. Let's keep up the good vibes and forward momentum -- exciting times for struct bio!
Being part of a community has always been essential for me. Finding a vibrant structural biology community in New York shaped my decision to stay in this City. Thank you @natsmb.nature.com for the opportunity to share it on your pages.
New online: New York City’s structural biology mosaic
November 5, 2025 at 10:38 PM
Props to my colleague here at the @asrc-gc.bsky.social , @fravallese.bsky.social , for this wonderful piece about the uniquely strong structural biology community here in NYC. I often feel lucky to be here. Let's keep up the good vibes and forward momentum -- exciting times for struct bio!
Our lab did a JC on this innovative preprint by @mcagiada.bsky.social @sokrypton.org @lindorfflarsen.bsky.social et al. abt predicting AF2 for prot sc flex: www.biorxiv.org/content/10.1... It inspired me to try my hand at a @prereview.bsky.social "preprint review"! prereview.org/reviews/1704...
AF2χ: Predicting protein side-chain rotamer distributions with AlphaFold2
The flexibility of protein side chains is an essential contributor of conformational entropy and affects processes such as folding, stability and molecular interactions. Structure determination experi...
www.biorxiv.org
September 3, 2025 at 6:19 PM
Our lab did a JC on this innovative preprint by @mcagiada.bsky.social @sokrypton.org @lindorfflarsen.bsky.social et al. abt predicting AF2 for prot sc flex: www.biorxiv.org/content/10.1... It inspired me to try my hand at a @prereview.bsky.social "preprint review"! prereview.org/reviews/1704...
I'm pleased to report that my job title has changed! (Except for the 1st 3 letters of the 1st word & the entire 2nd word... 😉) keedylab.org/members/ Grateful that I get to do fun science & train young scientists in an inspiring environment here at @asrc-gc.bsky.social & @ccnyscience.bsky.social!
keedylab.org
September 2, 2025 at 3:38 PM
I'm pleased to report that my job title has changed! (Except for the 1st 3 letters of the 1st word & the entire 2nd word... 😉) keedylab.org/members/ Grateful that I get to do fun science & train young scientists in an inspiring environment here at @asrc-gc.bsky.social & @ccnyscience.bsky.social!
Summer 2025 #keedylab news round-up: come read about what we did on our summer vacation! keedylab.org/news/
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
News | Keedy Lab
keedylab.org
August 13, 2025 at 8:43 PM
Summer 2025 #keedylab news round-up: come read about what we did on our summer vacation! keedylab.org/news/
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
Associated with this website update, I also embedded the lab's Bluesky feed on the website's news page -- thus creating an infinite cycle of delightful lab news links 🔁 💯
We wrote a review article about dynamics, allostery, and function in the PTP enzyme family! Covers experimental and computational approaches, regulatory domains & mechanisms, mutations, ligands, etc. Was hard to fit in ~all the cool advances in recent years!... pmc.ncbi.nlm.nih.gov/articles/PMC...
Orchestrating function: concerted dynamics, allostery, and catalysis in protein tyrosine phosphatases
Protein tyrosine phosphatases (PTPs) are a family of enzymes that play critical roles in intracellular signaling and regulation. PTPs are conformationally dynamic, exhibiting motions of catalytic loop...
pmc.ncbi.nlm.nih.gov
August 6, 2025 at 12:15 AM
We wrote a review article about dynamics, allostery, and function in the PTP enzyme family! Covers experimental and computational approaches, regulatory domains & mechanisms, mutations, ligands, etc. Was hard to fit in ~all the cool advances in recent years!... pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Daniel Keedy
Gift link
www.nytimes.com/2025/07/22/s...
www.nytimes.com/2025/07/22/s...
Amid Fear of Retaliation, N.S.F. Workers Sign Letter of Dissent
www.nytimes.com
July 23, 2025 at 1:39 AM
Gift link
www.nytimes.com/2025/07/22/s...
www.nytimes.com/2025/07/22/s...
Happy to say our recent @biorxiv-biophys.bsky.social preprint about 3 unexpected structures of STEP, in its new & improved form, is now published at Proteins! pubmed.ncbi.nlm.nih.gov/40616465/ & doi.org/10.1002/prot...
Three STEPs Forward: A Trio of Unexpected Structures of PTPN5 - PubMed
Protein tyrosine phosphatases (PTPs) play pivotal roles in myriad cellular processes by counteracting protein tyrosine kinases. Striatal-enriched protein tyrosine phosphatase (STEP, PTPN5) regulates s...
pubmed.ncbi.nlm.nih.gov
July 7, 2025 at 7:12 PM
Happy to say our recent @biorxiv-biophys.bsky.social preprint about 3 unexpected structures of STEP, in its new & improved form, is now published at Proteins! pubmed.ncbi.nlm.nih.gov/40616465/ & doi.org/10.1002/prot...
Reposted by Daniel Keedy
250 years ago, Americans rejected the rule of a mad king.
In two days, we’re taking to the streets again to say NO KINGS.
2,000 peaceful protests are planned in small towns and major cities across the country. Join your community on Saturday for #NoKings Day: www.nokings.org?SQF_SOURCE=i...
In two days, we’re taking to the streets again to say NO KINGS.
2,000 peaceful protests are planned in small towns and major cities across the country. Join your community on Saturday for #NoKings Day: www.nokings.org?SQF_SOURCE=i...
June 12, 2025 at 4:23 PM
250 years ago, Americans rejected the rule of a mad king.
In two days, we’re taking to the streets again to say NO KINGS.
2,000 peaceful protests are planned in small towns and major cities across the country. Join your community on Saturday for #NoKings Day: www.nokings.org?SQF_SOURCE=i...
In two days, we’re taking to the streets again to say NO KINGS.
2,000 peaceful protests are planned in small towns and major cities across the country. Join your community on Saturday for #NoKings Day: www.nokings.org?SQF_SOURCE=i...
New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models
How do related proteins with a common fold perform diverse biological functions? Although the average structure may be similar, structural excursions from this average may differ, giving rise to allos...
www.biorxiv.org
May 27, 2025 at 7:23 PM
New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
www.biorxiv.org/content/10.1...
How do related proteins perform distinct functions despite sharing a similar structure?...
Reposted by Daniel Keedy
We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org.
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
Junior/Assistant/Associate/Full Specialist Positions Available
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
May 20, 2025 at 5:26 PM
We are looking to hire (yes, even in this economy!) a jr. specialist to train in protein prep/structural biology related to our AVOID-ome work as part of openadmet.org.
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
A great position for someone who is looking to be a tech for a few years before grad or med school.
aprecruit.ucsf.edu/JPF05424
Reposted by Daniel Keedy
The third episode of The Tortured Proteins Department is out now!
We chatted about grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms around code release, and the importance of giving kudos. @fraserlab.com
We chatted about grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms around code release, and the importance of giving kudos. @fraserlab.com
May 16, 2025 at 3:48 PM
The third episode of The Tortured Proteins Department is out now!
We chatted about grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms around code release, and the importance of giving kudos. @fraserlab.com
We chatted about grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms around code release, and the importance of giving kudos. @fraserlab.com
Reposted by Daniel Keedy
Definitely worth a read and a share...
🚨 This MUST READ essay and call to action spells out, in very clear terms, how the Trump administration could get away with slashing the NIH budget. NIH scientists and Dems in congress need to read and understand it. This is where we win or lose the battle to save the NIH and US science. 🧪 🧠 🧬 🔊
The NIH budget is on a fast track to disaster
An NIH insider explains what Republicans are likely to do next, and what we can do
donmoynihan.substack.com
April 28, 2025 at 1:00 PM
Definitely worth a read and a share...
Reposted by Daniel Keedy
We're hiring for three positions:
Asst./Assoc./Prof. of Neuroscience: bit.ly/43ScWzE
Research Associate in the MRI Facility: bit.ly/3Ey1ONY
Asst./Assoc./Prof. of Photonics: bit.ly/4ijNVkh
Asst./Assoc./Prof. of Neuroscience: bit.ly/43ScWzE
Research Associate in the MRI Facility: bit.ly/3Ey1ONY
Asst./Assoc./Prof. of Photonics: bit.ly/4ijNVkh
April 21, 2025 at 1:33 PM
We're hiring for three positions:
Asst./Assoc./Prof. of Neuroscience: bit.ly/43ScWzE
Research Associate in the MRI Facility: bit.ly/3Ey1ONY
Asst./Assoc./Prof. of Photonics: bit.ly/4ijNVkh
Asst./Assoc./Prof. of Neuroscience: bit.ly/43ScWzE
Research Associate in the MRI Facility: bit.ly/3Ey1ONY
Asst./Assoc./Prof. of Photonics: bit.ly/4ijNVkh
Reposted by Daniel Keedy
Nothing else to say.
February 19, 2025 at 12:38 AM
Nothing else to say.
Reposted by Daniel Keedy
Roses are red
Violets are blue
If you fall in love with your hypothesis
You’ll be biased to prove it true
🧪
Violets are blue
If you fall in love with your hypothesis
You’ll be biased to prove it true
🧪
February 14, 2024 at 12:45 PM
Roses are red
Violets are blue
If you fall in love with your hypothesis
You’ll be biased to prove it true
🧪
Violets are blue
If you fall in love with your hypothesis
You’ll be biased to prove it true
🧪
Reposted by Daniel Keedy
Are you interested in understanding how the wiggles & jiggles of proteins impact the thermodynamics of ligand binding or catalysis? Well, you are in luck! We are searching for a postdoc to explore these concepts. More details: www.vanderbilt.edu/postdoc/pros... or email stephanie@wankowiczlab.com
Current Opportunities at Vanderbilt
Vanderbilt is committed to providing a meaningful, robust experience for postdocs. Below is a list of currently available postdoctoral opportunities. Postdocs interested in applying for a specific pos...
www.vanderbilt.edu
January 21, 2025 at 11:16 PM
Are you interested in understanding how the wiggles & jiggles of proteins impact the thermodynamics of ligand binding or catalysis? Well, you are in luck! We are searching for a postdoc to explore these concepts. More details: www.vanderbilt.edu/postdoc/pros... or email stephanie@wankowiczlab.com
Reposted by Daniel Keedy
"Being a first-generation college student, I’m excited by the idea of training & mentoring other first-generation students & taking on this important responsibility." —Prof. Francesca Vallese. Get to know SBI's new member & her critical area of research. bit.ly/3UYHKcN @thegraduatecenter.bsky.social
December 11, 2024 at 8:25 PM
"Being a first-generation college student, I’m excited by the idea of training & mentoring other first-generation students & taking on this important responsibility." —Prof. Francesca Vallese. Get to know SBI's new member & her critical area of research. bit.ly/3UYHKcN @thegraduatecenter.bsky.social
Check out our lab's first pub since the great X->Bsky exodus! We used crystallography under different conditions to map new conformational & chemical features of an atypical phosphatase enzyme. Fantastic work by Liliana, Ali, and Blake as well as collabs near (Bishop) & far (Tautz)!
Three STEPs forward: A trio of unexpected structures of PTPN5 https://www.biorxiv.org/content/10.1101/2024.11.20.624168v1
Three STEPs forward: A trio of unexpected structures of PTPN5 https://www.biorxiv.org/content/10.1101/2024.11.20.624168v1
Protein tyrosine phosphatases (PTPs) play pivotal roles in myriad cellular processes by counteractin
www.biorxiv.org
November 21, 2024 at 7:27 PM
Check out our lab's first pub since the great X->Bsky exodus! We used crystallography under different conditions to map new conformational & chemical features of an atypical phosphatase enzyme. Fantastic work by Liliana, Ali, and Blake as well as collabs near (Bishop) & far (Tautz)!
I'm excited to share our lab's latest @biorxiv-biophys.bsky.social preprint: www.biorxiv.org/content/10.1... This was a really rewarding collaboration between many folks here at the CUNY ASRC and the Farooqi lab at Cambridge, bridging the human genetics of obesity and some cool molecular biophysics!
Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
August 8, 2024 at 1:59 AM
I'm excited to share our lab's latest @biorxiv-biophys.bsky.social preprint: www.biorxiv.org/content/10.1... This was a really rewarding collaboration between many folks here at the CUNY ASRC and the Farooqi lab at Cambridge, bridging the human genetics of obesity and some cool molecular biophysics!
Reposted by Daniel Keedy
We were incredibly disappointed with the lack of code or executable accompanying the publication of AF3 in @Nature . This contradicts scientific principles of the ability to evaluate, use, and build upon existing work. zenodo.org/records/1117.... Sign to endorse: docs.google.com/forms/d/e/1F...
AlphaFold3 Transparency and Reproducibility
Link for endorsement signatures: https://forms.gle/d47w29eGHeL1ejXw9
zenodo.org
May 11, 2024 at 10:53 PM
We were incredibly disappointed with the lack of code or executable accompanying the publication of AF3 in @Nature . This contradicts scientific principles of the ability to evaluate, use, and build upon existing work. zenodo.org/records/1117.... Sign to endorse: docs.google.com/forms/d/e/1F...
Earthquake just now in upper Manhattan... Biggest I've ever felt (and I lived in the Bay Area for 5 years)... Reports of the same thing simultaneously in Queens... Everyone here is safe!...
April 5, 2024 at 2:29 PM
Earthquake just now in upper Manhattan... Biggest I've ever felt (and I lived in the Bay Area for 5 years)... Reports of the same thing simultaneously in Queens... Everyone here is safe!...
Got back last night from a great visit to Baylor Chemistry & Biochemistry! Thanks to Jonathan Clinger for inviting + hosting -- and was nice to meet @trakselis.bsky.social (& many others not on Bsky)!
March 24, 2024 at 3:41 PM
Got back last night from a great visit to Baylor Chemistry & Biochemistry! Thanks to Jonathan Clinger for inviting + hosting -- and was nice to meet @trakselis.bsky.social (& many others not on Bsky)!
Just returned from a wonderful visit to UC Irvine Molecular Biology & Biochemistry! Was nice to be back in the UC system for a day, meet many great folks doing cool science, and get to talk about what we've been up to in the Keedy lab. Special thanks to Melanie Cocco for hosting!
March 10, 2024 at 3:47 PM
Just returned from a wonderful visit to UC Irvine Molecular Biology & Biochemistry! Was nice to be back in the UC system for a day, meet many great folks doing cool science, and get to talk about what we've been up to in the Keedy lab. Special thanks to Melanie Cocco for hosting!
Reposted by Daniel Keedy
This is the 1957 plasticine model of myoglobin by Kendrew. It is based on X-ray data and shows the polypeptide chain as a large 💩. It is an aesthetic failure but, as the first-ever protein model, it was a huge breakthrough in protein structure 🙂
collection.sciencemuseumgroup.org.uk/objects/co13...
collection.sciencemuseumgroup.org.uk/objects/co13...
February 5, 2024 at 1:57 PM
This is the 1957 plasticine model of myoglobin by Kendrew. It is based on X-ray data and shows the polypeptide chain as a large 💩. It is an aesthetic failure but, as the first-ever protein model, it was a huge breakthrough in protein structure 🙂
collection.sciencemuseumgroup.org.uk/objects/co13...
collection.sciencemuseumgroup.org.uk/objects/co13...
'024 New Year lab news roundup: keedylab.org/news/ It's not too late to say Happy New Year yet, right?!
January 30, 2024 at 9:31 PM
'024 New Year lab news roundup: keedylab.org/news/ It's not too late to say Happy New Year yet, right?!