Daniel Keedy

Vibrant color portrait of Jane S. Richardson, the visionary biophysicist and artist who revolutionized structural biology with her invention of ribbon diagrams. She gazes warmly at the camera with a bright, knowing smile that radiates quiet brilliance and decades of curiosity. Her silver-blonde hair woven with gentle waves. Large, elegant dangling earrings catch the light, and she wears a richly patterned brown blouse embroidered with intricate turquoise paisley motifs and delicate beadwork that echoes the molecular elegance she has spent her life depicting. Behind her floats a luminous, dreamlike backdrop of glowing molecular structures--interlocking hexagonal and ribbon-like forms in electric blues, teals, and greens--blending science and art in a single, living canvas.

Hand-drawn and hand-colored (by Jane Richardson) scientific artwork known as a Richardson ribbon diagram (or “ribbon model”), one of the iconic visual inventions of Jane Richardson that transformed the way we see and understand protein structures. A graceful, three-dimensional tangle of protein backbone ribbons twists and spirals through space, rendered in soft pencil lines and luminous watercolor hues. Smooth golden-brown coils represent α-helices that curl like elegant ribbons, while broad teal-green arrows trace the flat, pleated strands of β-sheets slicing through the molecule with directional purpose. Thin, looping golden threads connect the secondary structures, creating a delicate, almost dance-like choreography of biology’s hidden architecture. The entire form is framed by a simple olive-green mat and dark border, giving the drawing the quiet dignity of both fine art and precise scientific illustration—a timeless bridge between molecular reality and human imagination.

Jane Richardson was born #OTD in 1941

+ Developed the Richardson (ribbon) diagram to represent proteins' 3D structure (becoming a standard representation for protein structures)
+ MacArthur Fellow, 1985
+ Elected, Nat'l Academy of Sciences, 1991
+ President, Biophysical Society, 2012

#WomenInSTEM

Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain Structure-based drug design has traditionally focused on optimizing static, enthalpic interactions between ligands and proteins or on displacing binding site solvent molecules to entropically favor bi...

New preprint! Entropy drives molecular recognition, yet most structure-based drug design ignores it because it is difficult to measure. X-ray crystallography captures ensembles, not single structures. Can we extract thermodynamically meaningful entropy from them?

www.biorxiv.org/content/10.1...

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!

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

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...

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 !

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...

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...

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

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 🔁 💯

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...

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...

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

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

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...

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...

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...

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!

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!

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...

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

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...

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...

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...

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?...

Junior/Assistant/Associate/Full Specialist Positions Available University of California, San Francisco is hiring. Apply now!

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

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

Definitely worth a read and a share...

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

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

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

Nothing else to say.

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

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

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...

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

A seminal and thought-provoking paper! Congrats on the anniversary.

A headshot photo of Professor Francesca Vallese.

"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