Ashutosh Kumar

Can we design mutations that predictably bias proteins towards desired conformational states? Today in @ScienceMagazine, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations. science.org/doi/10.1126/sc…

(Part 1/2) Excited to share that our work, led by PhD student Keerthivasan Muthukumar (@kvasan452) and postdoc Dr. Dinesh S. Devarajan (@Dsundara993), is now published in PNAS (pnas.org/doi/10.1073/pn…).

Dystonia-associated Torsins sustain CLCC1 function to promote membrane fusion of the nuclear envelope for NPC biogenesis biorxiv.org/content/10.110… #biorxiv_cellbio

I am hiring at the PhD or Postdoc level. I am looking for motivated candidates willing to work on a challenging project at the frontiers of what we understand of protein colloidal stability.

Our collaborative work "The #Martini3 #Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior" is now published in #ACSCentralScience! 🎉 📄 Read: pubs.acs.org/doi/10.1021/ac… 💾 GitHub: github.com/Martini-Force-… #MolecularDynamics #Biophysics #Simulations #Lipids

If heterochromatin is really a liquid-like condensate, why is it not spherical? We investigated whether mechanical interactions between a condensate and a fiber network can explain the variety of morphologies seen in phase-separated nuclear compartments. biorxiv.org/content/10.110…

Excited to share the new work from the Carvalho lab @Dunn_School! 🎉This was part of my PhD & a collaboration with the @LabVanni & Ernst labs! Big thanks to everyone involved! 🙌 Read more: doi.org/10.1083/jcb.20… (1/2)

Join our interdisciplinary team developing computational approaches to understand and engineer biomolecular condensates. We’re looking for a postdoc—please apply or share with interested persons! 👩🏽‍💻💧🧬 puwebp.princeton.edu/AcadHire/apply…

Nature research paper: Structural basis of lipid transfer by a bridge-like lipid-transfer protein go.nature.com/4itODM4

Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang: nature.com/articles/s4146…

ABHD17 enzymes remove fatty acids from #membrane proteins like NRas. New work from Holme, Sapia, @LabVanni, Conibear @UBC et al. show that their activity depends on two mobile regions: an S-acylated N-terminal helix and a loop. hubs.la/Q036MbQS0

After some work, we’ve now made the @github for our #Martini3 #LNP models and protocols publicly available: github.com/Martini-Force-… We also have a new @ChemRxiv with some minor updates: chemrxiv.org/engage/chemrxi… #LipidNanoparticles #MD #DrugDelivery #mRNA #Simulation

In collaboration with @BanerjeeLab_UB, we dive a little deeper into the microscopic interactions and sequence patterns shaping condensate activation energies pubs.acs.org/doi/10.1021/ac…. For more context, see also our prior work science.org/doi/10.1126/sc…

#HighlightOfTheWeek MD simulation with a flow. #compchem pubs.acs.org/doi/10.1021/ac…

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @MSFTResearch AI for Science. #ML #AI #NeuralNetworks #Biology #AI4Science biorxiv.org/content/10.110…

We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered??? nature.com/articles/s4158…

A coarse-grained model of disordered RNA for simulations of biomolecular condensates biorxiv.org/cgi/content/sh… #biorxiv_biophys

@JiaqiZhuDartmth and I are excited to share our new manuscript characterizing the conformational ensembles of covalent adducts formed by a disordered protein and small molecule drugs biorxiv.org/content/10.110… Code + Ensembles: github.com/paulrobustelli…

@GeaCereghetti Congratulations, Gea !

🎉Thrilled to receive the Lopez-Loreta Prize 2024! This award allows me to establish my own research team and tackle key questions on protein aggregation. Grateful to the Foundation, my mentors Tuomas & Matthias, and all amazing colleagues who've supported me in this journey!✨️

Entropy can contribute to stability of RNA clusters! Find out more from Dilimulati Aierken’s new paper! Thrilled to have this work published @JCIM_JCTC pubs.acs.org/doi/10.1021/ac…