Maksim Kalutskii

Our review on Integrative modelling of biomolecular dynamics 💃 is now live at COSB

We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics

With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...

TT in Experimental Biophysics

The Danish Institute for Advanced Study and the Dept of Physics, Chemistry and Pharmacy at the University of Southern Denmark is hiring a tenure track Assistant Professor in Biophysics or a related discipline

fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com/hcmUI/Candid...

The Frankfurt Institute for Advanced Studies (FIAS) and the newly funded Cluster of Excellence SCALE are seeking several Independent Research Group Leaders to drive theoretical and computational research in molecular and cellular life science.

fias.institute/de/das-fias/...

Human spastin functions as an ATPase-independent microtubule nucleator via ring-stack formation Microtubule severing enzyme spastin plays pivotal roles in cytokinesis and neuronal outgrowth, and its mutations cause hereditary spastic paraplegia (HSP). Here we show that, at physiological tubulin ...

Our latest work is out in biorxiv! 😊

We show that human spastin, a microtubule severing enzyme, behaves completely differently in presence of free tubulin - it forms tubulin ring stack and promotes de novo microtubule nucleation.

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

Across (Conformational) Space and (Relaxation) Time: Using Coarse-Grain Simulations to Probe the Intra- and Interdomain Dynamics of the Tau Protein The biological importance of intrinsically disordered proteins (IDPs) has been established for over two decades, yet these systems remain difficult to characterize, as they are better described by conformational ensembles instead of a single reference structure for their folded counterparts. Tau is a prominent member of the IDP family, which sees its cellular function regulated by multiple phosphorylation sites and whose hyperphosphorylation is involved in neurodegenerative diseases such as Alzheimer’s. We used coarse-grain MD simulations with the CALVADOS model to investigate the conformational landscape of tau without and with phosphorylations. Characterizing the local compactness of IDPs allows us to highlight how disorder comes in various flavors, as we can define different domains along the tau sequence. We define the IDP’s Statistical Tertiary Organization (STO) as the average spatial arrangements of domains, which constitute an extension of the tertiary structure of folded proteins. We also use IDP-specific metrics to characterize the local curvature and flexibility of tau. Comparing the local flexibilities with T2 relaxation times from NMR experiments, we show how this metric is related to the protein dynamics. A curvature and flexibility pattern in the repeat domains can also be connected to tau binding properties, without having to explicitly model the protein’s interaction partner. Finally, we rediscuss the original paperclip model that describes the spatial organization of tau and how phosphorylations impact it. The resulting changes in the protein intradomain and interdomain interaction pattern allow us to propose experimental setups to test our hypothesis.

"Across (Conformational) Space and (Relaxation) Time", @marienj.bsky.social's latest work, is now out in J. Phys. Chem. B @pubs.acs.org. In this paper, we used coarse-grain simulations with the CALVADOS model to investigate the dynamics of a large IDP.
pubs.acs.org/doi/10.1021/...

Very excited to present OpenCGChromatin🔥🔥🔥

A new coarse-grained model that probes full chromatin condensates at near-atomistic resolution to reveal the molecular regulation of chromatin structure and phase separation

Brilliantly led by @kieran-russell.bsky.social, with the Rosen and Orozco groups

NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations DNA's physical properties play a central role in genome organization and regulation, but simulating its behavior across biologically relevant scales remains a major computational challenge. Coarse gra...

Our preprint on a single-bead-per-nucleotide DNA model is live! This model reproduces both atomistic simulations and persistent length for a variety of sequences. It's compatible with openMM, allowing for highly efficient GPU simulations.
www.biorxiv.org/content/10.1....

An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies www.biorxiv.org/content/10.1...

👉Applications will be reviewed on a rolling basis until the #postodc or #phd #position is filled. 📩 Send us your message to explain why you are a great candidate to join the group "Computational Biomolecular Dynamics" of Bert de Groot @mpi-nat.bsky.social 🔗 www.mpinat.mpg.de/degroot #compbiophys

🔬 CECAM Workshop: “Integrative and Multiscale Modelling Approaches to Illuminate CryoEM/ET Data”

Join us in Toulouse, 24–26 March 2026, to explore how molecular simulations, AI tools, can be integrated to cryo-EM and cryo-ET data.

🧬 Selection: brief CV + motivation letter required.

Apply 👇

Are you looking for a PhD opportunity? Or would you like to start your postdoc after having earned your doctorate?
Our Department of Theoretical and Computational Biophysics @compbiophys.bsky.social is hiring: ⬇️

Huge thanks to everyone who was involved: Maxim @maxotubule.bsky.social Helmut @compbiophys.bsky.social and especially Carter @carterjwilson.bsky.social!

📜 New preprint! We developed PoGö, an algorithm to optimize the essential dynamics of GöMartini proteins based on all-atom simulations: www.biorxiv.org/content/10.1...

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org

Check out our new work, led by talented @janhuemar.bsky.social, where we uncover that pioneer factor Oct4 remodels chromatin for DNA access not by opening it but by exploiting nucleosome breathing and forming clusters 🔥🔥🔥

We (@sobuelow.bsky.social) developed AF-CALVADOS to integrate AlphaFold and CALVADOS to simulate flexible multidomain proteins at scale

See preprint for:
— Ensembles of >12000 full-length human proteins
— Analysis of IDRs in >1500 TFs

📜 doi.org/10.1101/2025...
💾 github.com/KULL-Centre/...

Dick is one of the most thoughtful folks in cell biology--this is a must read for anyone interested in microtubules!

Eye of the mantis shrimp. Bali/Amed with @cecclementi.bsky.social

Helmut Grubmüller

📢 We are hiring #PhD students and #Postdocs at the
@mpi-nat.bsky.social in
in the Department of Theoretical and Computational #Biophysics in Göttingen 🇩🇪! 🔗 check our current job adverts at www.mpinat.mpg.de/grubmueller and find your project. Submit your #application today! #job

👉 Open #PhD and #Postdoc positions in #computational #biophysics @mpi-nat.bsky.social in Göttingen 🇩🇪 in the Computational Biomolecular Dynamics group of Bert deGroot for several projects! Applications welcome! 🔗https://www.mpinat.mpg.de/5088717/24-25?c=645962 📝ausschreibung24-25@mpinat.mpg.de

Laser flash melting cryo-EM samples to overcome preferred orientation - Nature Methods Individual proteins tend to adopt preferred orientations when subjected to vitrification for cryo-electron microscopy analysis. A laser flash melting procedure followed by rapid revitrification provid...

A laser flash melting procedure, followed by rapid revitrification, provides a simple approach to help mitigate the preferred orientation problem that plagues cryo-EM analysis.

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

We are recruiting 2 postdocs to work on bacterial motility using a combination of cryoEM, FLM and MD. An exciting collaboration with Kirsty Wan @micromotility.bsky.social Wolfram Moebius @wolframmoebius.bsky.social and Daniel Kattnig. Please see links in the thread below!

#PostDoc opportunity in data-driven #SynChem planning at MIT (Cambridge MA USA) duration: 2 years #cheminformatics #DataScience #CompChem #ChemPostDoc #PostDocJobs #chemsky 🧪
coley.mit.edu/positions

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