Danny Evans

Now on to my next adventure: finding a postdoc lab! If you have an opening and think I might be a good fit, please do not hesitate to contact me!

3/3 Here's the Github link to EVADE: github.com/laulab-johnsho…

1/3 Just released my latest preprint! Introducing EVADE - a Python package designed for analyzing pocket volumes and dihedral correlations. Using EVADE, I uncovered statistical pitfalls and novel insights into the enigmatic protein 3CLPro. doi.org/10.1101/2024.0…

@adele_valeria I think evaluating whether a place is "better"/"worse" is a hard problem. A simple number ranking would struggle to capture the full range of factors. Saying "scores low on this particular scale" seems more accurate than "worst".

How appropriate is it to use the word "worst" in this context? What do you think?

@elisew00 Thanks a lot!

@danielJEvans That is so cool!! It came out great!! (Wishing I could do this for my RNA structures)

In 2020 I got a CNC machine for woodcarving. I recently discovered how to carve protein structures. It’s fun when an unrelated interest intersects with my work! (I chose ubiquitin as a test case b/c it’s small and well-known. The carving process should work for most proteins.)

The Program in Molecular Biophysics @JohnsHopkins is finally on Twitter! Follow us for news about our terrific graduate students and faculty. You can find out about our Ph.D. program at pmb.jhu.edu . Please follow and RT!

New preprint from the Lau Lab and @Lab_FURUKAWA. We used molecular dynamics simulations and electrophysiology (@TsungHan_Chou) to study the role of D-serine binding to NMDAR LBDs.

So excited to share our lab’s newest paper with @Lab_FURUKAWA, including some of my thesis work using MD simulations and network modeling to study Fab binding to the NMDAR. Thankful to have worked with such an amazing team!

@fried_lab's first foray in structural bioinformatics is out on @github. Great work by new grad student, @ManriquezEdgar. DomainMapper annotates protein domain structure, and properly labels non-contiguous, insertional, and circularly permuted domains. github.com/FriedLabJHU/Do…

(Actually Albert Lau is my PI, not a co-worker... but including all that in a single well-structured tweet seemed difficult. Thus I wrote a simpler tweet, and added this long clarifying footnote. David Foster Wallace might approve!)

The TACTICS paper is published in JCIM! Thanks to @SanimRahman4 @rem_yo @morgbeck @0xAfif (and David Cao, Milan Patel, and Albert Lau, whose twitters I don't know) for being great co-workers!

@KennyMarincin Congratulations; that's awesome!

Just submitted my first, first-author manuscript as a PhD student. They don't prepare you for this amount of relief. #phdchat

@CWolberger @SanimRahman4 @remy_yo Thanks a lot!

Retweeting this because I neglected to tag student @SanimRahman4 who is co-first author! 🎉 Also big shout-out to #biophysics students @remy_yo and Dan Evans.

#BPS2021 is now underway... I'm excited to hear about the latest work from @rem_yo, shown in a Thursday 11:15-11:30 talk "Role of D-Serine Binding To The NMDA Receptor Ligand-Binding Domain". Having seen some of the data, I can assure you it's worth attending!

We developed ML-based software for finding cryptic sites. We applied the method to 3 proteins: two from SARS-CoV-2, and one from yersinia pestis. Thanks to everyone who contributed to the project! The preprint is available at disq.us/t/3v1sacp