Maksim Kalutskii

Computational discovery of novel oxide-based X-ray detectors at University of Birmingham on FindAPhD.com PhD Project - Computational discovery of novel oxide-based X-ray detectors at University of Birmingham, listed on FindAPhD.com

PLEASE REPOST: We have a 4-year, fully funded PhD studentship focussed on using computational chemistry to find new and improved oxides for X-ray detection, to start in October 2025. findaphd.com/phds/project.... This is open only to UK nationals.

A few highlights from our new preprint:

On taxol-stabilized microtubules In vitro, wild-type (WT) and phosphor-resistive (AP) tau form well-defined envelopes, while phosphomimetic (E14) tau does not bind cooperatively.

Diffusing protein binders to intrinsically disordered proteins - Nature Using RFdiffusion, a general method for targeting intrinsically disordered proteins and regions for protein design has been developed.

Nature research paper: Diffusing protein binders to intrinsically disordered proteins

go.nature.com/4lSCdzE

Intrinsic disorder comes in various flavors ! Using CALVADOS simulations of the Tau protein, we reveal that its disordered dynamics can be interpreted at both residue and domain scales, and that addition of phosphorylations impact both

By @sacquin-mo.bsky.social , Chantal Prévost and I

Our paper on:

A coarse-grained model for simulations of phosphorylated disordered proteins

(aka parameters for phospho-serine and -threonine for CALVADOS)

is now published in Biophysical Journal

authors.elsevier.com/a/1lTcE1SPTB...

@asrauh.bsky.social @giuliotesei.bsky.social & Gustav Hedemark

Navigating protein landscapes with a machine-learned transferable coarse-grained model - Nature Chemistry The development of a universal protein coarse-grained model has been a long-standing challenge. A coarse-grained model with chemical transferability has now been developed by combining deep-learning m...

Our development of machine-learned transferable coarse-grained models in now on Nat Chem! doi.org/10.1038/s415...
I am so proud of my group for this work! Particularly first authors Nick Charron, Klara Bonneau, Aldo Pasos-Trejo, Andrea Guljas.

Arriën & Giulio's paper on

A coarse-grained model for disordered proteins under crowded conditions

(that is the CALVADOS PEG model) is now published in final form:
dx.doi.org/10.1002/pro....

@asrauh.bsky.social @giuliotesei.bsky.social

Ever wondered how one can design dynamics into proteins? Check out our work on flexibility conditioned protein structure design at ICML (Poster W-109, Thu. 11am)!

We introduce a flow matching framework for generating protein backbones with custom per-residue flexibility, validated by 300ns of MD.

Great work!

A Minimal Chemo-mechanical Markov Model for Rotary Catalysis of F1-ATPase https://www.biorxiv.org/content/10.1101/2025.06.26.661389v1

You want to make your simulations reactive, at little cost? Try KIMMDY. Don't hesitate to reach out if you want to include your favorite chemistry. Super happy to see this online, kudos to the team!

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

Time’s running out! Lead generative AI research for molecular dynamics in our lab AIMLeNS.
- Scale our NeurIPS/ICLR-published implicit transfer operators to revolutionize simulations.
Postdoc position closes 10. July. Apply now:
www.chalmers.se/en/about-cha...

Microtubule dynamics are defined by conformations and stability of clustered protofilaments | PNAS Microtubules are dynamic cytoskeletal polymers that add and lose tubulin dimers at their ends. Microtubule growth, shortening, and transitions betw...

Have a great D2@ #EBSA2025 in Rome🫠! Here are the posters of today's session: 📌Maksim @maksimkalutskii.bsky.social is presenting (P-2.195) his project addressing #Microtubule Dynamics Are Defined by Conformations and Stability of Clustered #Protofilaments 📜🔗 www.pnas.org/doi/10.1073/...

Complete computational design of high-efficiency Kemp elimination enzymes - Nature We present a computational approach to the design of high-efficiency enzymes with catalytic parameters comparable to natural enzymes, enabling programming of stable, high-efficiency, new-to-nature Kem...

Our latest work is a collaboration led by Sarel Fleishman and Dina Listov, with Eva Vos, Andrej Berg, Gyula Hoffka and others. We present a fully computational workflow for designing highly proficient enzymes in TIM barrel folds. Read more here:

www.nature.com/articles/s41...

🌟 We are hiring! Seeking a postdoc to use molecular dynamics and AI to understand how ion channels are regulated by membrane lipids 🌟

Join us at #scienceanu with amazing collaborators and great working conditions!

Email me (karri.anu.edu.au) or apply here (tiny.cc/corry). Please share & repost!

This paper combines two sort-of-crazy (in the best sense) approaches in cryoEM sample preparation:
(1) Native, soft-landing electrospray ion beam deposition, followed by (2) deposition of amorphous ice, and reheating and freezing by laser flash melting. Has potential for time-resolved studies.

Efficient mRNA delivery to resting T cells to reverse HIV latency - Nature Communications Resting T cells are difficult to manipulate, and are a reservoir for latent HIV. Here, the authors develop a lipid nanoparticle formulation with the ability to transfect resting primary human T cells,...

Breakthrough in HIV latency reversal. A lipid nanoparticle co-formulated with an ionizable lipid and β-sitosterol delivers mRNA encoding HIV Tat or CRISPRa machinery directly into resting T cells. The approach reactivates latent HIV ex vivo without toxic effects or T cell activation.

the magic growing/shrinking GTP/GDP switch lies in the differential ability to bend out of plane and hold on neighbours.
Alone you go faster, together we go further.

@turnerb-123.bsky.social , first author of this manuscript, is now on bluesky, please follow him to learn about the latest developments in modelling Mtb cell wall.

I would like to mention here all the hard work done by Turner to model these very complex and novel systems. Congrats Turner!

Happy to contribute to this fantastic work by @maksimkalutskii.bsky.social and @maxotubule.bsky.social!
www.pnas.org/doi/abs/10.1...

Excited to share our latest work in @pnas.org! Combining simulations and cryo-ET, we reveal how microtubules decide between growth and shortening. doi.org/10.1073/pnas... @maksimkalutskii.bsky.social @vladimirvolkov.bsky.social @compbiophys.bsky.social @mpi-nat.bsky.social @qmul.ac.uk @dundee.ac.uk.

Figure outlining our approach to study changes in protein folding in condensates by simulations of differential partitioning of folded and unfolded proteins

The ability to model both folded domains and disordered regions in condensates means that we can now begin to use CALVADOS simulations to ask how and why the condensate environment changes protein folding stability 🧪
doi.org/10.1002/pro....

Helly from Severance “the numbers were scary”

Numbers being thrown in the bin on a retro computer screen

Altmetric score and weightings

Severance is a documentary about working at Altmetric

Our newest paper is out!

BioEmu is now easily accessible on Colab. Thank you @martinsteinegger.bsky.social and @jjimenezluna.bsky.social !!

@msftresearch.bsky.social

Martini3-IDP: improved Martini 3 force field for disordered proteins - Nature Communications Here, the authors introduce Martini3-IDP, a refined model for disordered proteins that addresses prior over-compact structures. Validated across diverse systems, it captures IDP interactions and biomo...

Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang: www.nature.com/articles/s41...

Gemma Solomon and I are looking for a postdoc to work across the two groups on modelling biological systems with a view to applications for quantum computing

More details about the project including how to apply in the link below. Deadline April 9 2025

candidate.hr-manager.net/ApplicationI...

CALVADOS now has parameters for phosphorylated amino acids

@asrauh.bsky.social @giuliotesei.bsky.social and Gustav Hedemark used a top-down approach in which we targeted experimental data to derive parameters or phosphorylated serine and threonine doi.org/10.1101/2025...

Figure from the paper illustrating sequence–ensemble–function relationships for disordered proteins. ML prediction (black) and design (orange) approaches are highlighted on the connecting arrows. Prediction of properties/functions from sequence (or vice versa, design) can include biophysics approaches via structural ensembles, or bioinformatics approaches via other hetero- geneous sources. The lower panels show examples of properties and functions of IDRs for predictions or design targets. ML, machine learning; IDRs, intrinsically disordered proteins and regions.

Our review on machine learning methods to study sequence–ensemble–function relationships in disordered proteins is now out in COSB

authors.elsevier.com/sd/article/S...
Led by @sobuelow.bsky.social and Giulio Tesei

PhD Position in Structural Biology (f/m/x)

An open #PhD position is available in my lab in Munich 🇩🇪 If you are interested in structural biology, #AlphaFold, or disordered proteins, see below for more details.

jobs.helmholtz-muenchen.de/jobposting/b...

#science #PhD #research