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Daniel Keedy @dkeedy.bsky.social · Sep 9

The process was super smooth to be honest -- no complaints here!

Daniel Keedy @dkeedy.bsky.social · Sep 4

Good to hear, Kresten -- we think the method is very cool (and plan to use it for some projects here soon)! Plenty of room to explore using the foundation you've built...

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Daniel Keedy @dkeedy.bsky.social · Sep 3

Thanks for encouraging this kind of thing more broadly @fraserlab.com, and for paving the way with another previous pre-review (pre-pre-review? 🤔) of the same preprint @stephanieaw.bsky.social !

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Daniel Keedy @dkeedy.bsky.social · Sep 3

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

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Daniel Keedy @dkeedy.bsky.social · Sep 2

Thx! Next time you're in Big Apple City or I'm in Beantown for sure...

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Daniel Keedy @dkeedy.bsky.social · Sep 2

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

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Daniel Keedy @dkeedy.bsky.social · Aug 13

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 🔁 💯

News | Keedy Lab

keedylab.org

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Daniel Keedy @dkeedy.bsky.social · Aug 6

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

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Reposted by Daniel Keedy

NER430 @ner430.bsky.social · Jul 23

Gift link
www.nytimes.com/2025/07/22/s...

Amid Fear of Retaliation, N.S.F. Workers Sign Letter of Dissent

www.nytimes.com

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Daniel Keedy @dkeedy.bsky.social · Jul 7

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

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Reposted by Daniel Keedy

Indivisible ❌👑 @indivisible.org · Jun 12

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...

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Daniel Keedy @dkeedy.bsky.social · May 27

We hope qFit + RINFAIRE is a useful comp struct bio pipeline for exploring how evolution has tinkered w/ allosteric wiring in prot fams, how collective dynamics "evolve" during iterative protein design, & how small-mol frag hits from X-ray screens tap into "nervous systems" of allosteric proteins!

Daniel Keedy @dkeedy.bsky.social · May 27

To validate RINFAIRE, we showed that fxnally impactful mutations from many PTPs are enriched near our network residues.

We also experimentally mutated residues that had varying seq conservation but were very interconnected per RINFAIRE. All muts altered catalysis -- & one surprisingly enhanced it!

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Daniel Keedy @dkeedy.bsky.social · May 27

We used RINFAIRE to map allosteric (re)wiring for the entire PTP enzyme family.

We found that PTPs have similar wiring that responds dynamically to catalytic motions & active-site vs. allosteric ligands, but differs among fxnally distinct PTPs.

All PTP supp files here: zenodo.org/records/1542...

Supplementary materials for RINFAIRE network analysis of qFit multiconformer models for PTP enzymes

These files are provided to recapitulate analyses in the manuscript titled "Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models".

zenodo.org

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Daniel Keedy @dkeedy.bsky.social · May 27

Enter RINFAIRE (Residue Interaction Networks From Alternate conformations In RElated structures)! 🏰 🐴 🍗

RINFAIRE builds "dynamic RINs" from qFit models, aligns them, and quantitatively compares them, including normalization, subsetting, etc.

The code is available here: github.com/keedylab/rin...

GitHub - keedylab/rinfaire: RINFAIRE: Dynamic residue interaction networks from protein crystallographic multiconformer models

RINFAIRE: Dynamic residue interaction networks from protein crystallographic multiconformer models - keedylab/rinfaire

github.com

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Daniel Keedy @dkeedy.bsky.social · May 27

We hypothesized that deviations from the avg struct may differ among homologs & diversify fxns e.g. catalysis & allostery.

Crystallographic alt confs from qFit offered a foothold, but we needed new tools to model networks of interacting alt confs and compare btw many related protein structures...

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Daniel Keedy @dkeedy.bsky.social · May 27

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?...

Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models

www.biorxiv.org

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Reposted by Daniel Keedy

James Fraser @fraserlab.com · May 20

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

Junior/Assistant/Associate/Full Specialist Positions Available

University of California, San Francisco is hiring. Apply now!

aprecruit.ucsf.edu

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Reposted by Daniel Keedy

Stephanie Wankowicz @stephanieaw.bsky.social · May 16

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

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Reposted by Daniel Keedy

Jeremy Berg @jeremymberg.bsky.social · Apr 28

Definitely worth a read and a share...

Rosa Lafer-Sousa @rosalafersousa.bsky.social · Apr 28

🚨 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

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Reposted by Daniel Keedy

Advanced Science Research Center at the CUNY Graduate Center @asrc-gc.bsky.social · Apr 21

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

A photo of the CUNY ASRC's exterior and the following text: "We are hiring a research assoc. and profs."

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Reposted by Daniel Keedy

Danielle Beckman @daniellebeckman.bsky.social · Feb 19

Nothing else to say.

"If you think research is expensive, try disease" - Mary Lasker

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Reposted by Daniel Keedy

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Feb 14

Roses are red
Violets are blue
If you fall in love with your hypothesis
You’ll be biased to prove it true
🧪

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Daniel Keedy @dkeedy.bsky.social · Feb 1

Protein design & fragment screening: two great flavors combined! Super cool... Congrats, all y'all!

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Reposted by Daniel Keedy

Stephanie Wankowicz @stephanieaw.bsky.social · Jan 21

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 [email protected]

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

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