Our manuscript on using the knot theory descriptor writhe to build kinetic models of IDP dynamics is now out in JCTC

pubs.acs.org/doi/full/10....

We think this approach establishes a new state-of-the-art for building markov state models of IDP dynamics.

Proud to share our manuscript:

"How small molecules stabilize oligomers of a phase-separating disordered protein"

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

by Jiaqi Zhu and Tommy Sisk, in collaboration with @borjaml.bsky.social , Stase Bielskute-Garcia & @xsalvatella1.bsky.social

Does anyone else think saying "this paper isn't a good fit for our journal" is quite a bit less silly than saying that a paper isn't a "striking advance" / "sufficiently timeless" / etc. ?.

Who is this goofy form letter language for exactly?

Happy to have contributed a few sections on NMR to this very practical and comprehensive community review on benchmarking force fields against experimental data.

Today Writhe, our favorite knot theory descriptor for characterizing IDP dynamics, is the star of the lab pumpkin for the annual department carving contest.

If you can make sense of the design— I’ll buy you a coffee, bao bun, or wheatgrass shot at the next conference. No substitutions.

Fun day at @dartmouthchem.bsky.social
serving buldak ramen and explaining the biophysics and structural biology of heat and capsaicin activation of the ion channels to celebrate @acs.org #NationalChemistryWeek.

Our work developing a maximum entropy reweighting method to refine all-atom ensembles of IDPs with extensive NMR and SAXS datasets is now out in @natcomms.nature.com:

rdcu.be/eKlK7

Led by @dartmouthchem.bsky.social graduate student Kaushilk Borthakur in collaboration with @bonomimax.bsky.social

Excited to share a new preprint:

"Monomer binding modes of small molecules that modulate the kinetics of hIAPP amyloid formation"

by graduate student Michelle Garcia together with post-doc Korey Reid.

Paper:
www.biorxiv.org/content/10.1...

Code + Ensembles: github.com/paulrobustel...

Want to run and analyze MD simulations of a disordered protein?

Check out our step-by-step guide (+ tutorial with code) for preparing, running and analyzing replica exchange solute tempering (REST2) simulations of IDPs with @gromacs.bsky.social and @plumed.org on arxiv!

arxiv.org/abs/2505.01860

Presenting one of my favorite manuscripts I've ever worked on:

"Characterizing structural and kinetic ensembles of intrinsically disordered proteins using writhe"

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

by Tommy Sisk, with a generative modeling component done in collaboration with @smnlssn.bsky.social

Thanks to my hosts @bonomimax.bsky.social, @xsalvatella1.bsky.social, @fabferrage.bsky.social, @rcrehuet.bsky.social & Gabi Heller for a wonderful sabbatical science tour of Barcelona, Paris and London! Until next time!

As an American who’s immigrant grandfather grew up in a New Jersey home with a dirt floor, I can’t quite explain the feeling I have when I walk past the pantheon to spend the afternoon discussing magnetic resonance with Parisian intellectuals.

Thanks @fabferrage.bsky.social for a great visit!

Proud to share:

"Ensemble docking for intrinsically disordered proteins"

from Dartmouth undergrad Anjali Dhar 24' and grad student Tommy Sisk. We present ensemble docking strategies for IDPs that, remarkably, seem to work!

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

Code: github.com/paulrobustel...

One note about the DiffDock *preprint* fracas: it seems like two of the main issues at hand

i) experienced researchers insisting on addition controls to justify claims

ii) objections to overly combative language and potentially misleading comparisons

are things that peer reviewed journals...

I’m looking for examples of the largest conformational changes that have been captured in ensemble docking or flexible docking approaches.

Can anyone point me to some good examples?

I'm excited to share a new manuscript with Jiaqi Zhu characterizing the conformational ensembles of covalent adducts formed by a disordered protein and small molecule drugs:
biorxiv.org/content/10.1...

Code + Ensembles:
github.com/paulrobustel...

Hello Bluesky.

I'm a little late to the new platform party because I was busy integrating a new #compchem scholar into our group.