David A Hendrix

Local Stability Compensation presents a bottom-up approach to RNA design, focusing on local interactions, compared to the top-down approach of global free energy minimization. Check out the paper for more! 4/4

Our large design libraries demonstrate that local stability compensation (net free energy of local substructure) correlates with folding accuracy through a Hill equation relationship. 3/4

We show that large, destabilizing loops are often immediately adjacent to more stabilizing stems in natural structures. We also show that designed structures fold more closely to their design when local stability compensation is considered. 2/4

Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA Abstract. RNA molecules adopt complex structures that perform essential biological functions across all forms of life, making them promising candidates for

We are excited to share a new publication w/ @JosephYesselman in @NAR_Open. RNA secondary structure prediction and design typically minimize the global free energy. We show that *local* stability compensation is a powerful way of designing RNA structures 1/4
academic.oup.com/nar/article/...

We hope to apply these methods to identify novel structures and to improve our RNA secondary structure meta-database, stay tuned for bpRNA-hub.

Although it isn't as accurate as our other alignment-based method bpRNA-align, (Published in RNA) it allows us to perform an initial clustering of 100s of thousands of structures, which we can refine, reducing the overall number of calculations
rnajournal.cshlp.org/content/29/5...

bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity AbstractMotivation. RNA secondary structure is often essential to function. Recent work has led to the development of high-throughput experimental probing

We are excited to share our latest publication, bpRNA-CosMoS, a k-mer based measure of #RNA structural similarity. This method allows us to perform millions of structural comparisons for clustering in a short amount of time. #OpenAccess in #Bioinformatics
academic.oup.com/bioinformati...

Sun shining and refracting through a skybridge between two brick buildings on a college campus.

Professor David Hendrix photographed this literal ray of spring equinox light shining through the skybridge connecting Cordley Hall and the Agriculture & Life Sciences Building. It’s a phenomenon he’s dubbed “BeaverHenge” because it only happens during the equinox. 🦫✨

Happy spring, everyone!

I caught a ray of light through the sky bridge between Ag & Life Sciences and Cordley Hall tonight around 7pm. Although the equinox was two days ago, it still works. It was the first day this week that wasn't too cloudy to see anything @oregonstate.edu #beaverhenge #gobeavs!

Great idea! So in other words use harder filament but use a heat gun to mold it into place. Sounds like a really cool plan

The issue is: how to you get it to pose into a 3D structure? That is something to work on. The flexible filament for the backbone allows it to be posed in various shapes, maybe transparent sting could hold it in place as a structure? Stay tuned for more!

After some attempts, it occurs to me that a 3D pen is the best method after all. 3D pen printing tends to be string- or stick-like, and is perfect for drawing molecular bonds. I'm experimenting with the technique and would like to further exaggerate the the atoms as round spheres

The design a graduate student in my lab came up with for a 3D printer had to be truncated to be printed, and required quite a lot of scaffolds. 3D printers need bulk, and the space-filling approach hides molecular details.

A desk with a 3D printed RNA polymer, 3D pen, a pair of scissors, and some 3D filament

I'm experimenting with 3D printing #RNA with a #3Dpen! It's a work in progress. I did this a few years back, and getting back into it.

#bioinformatics