Our new strategy for cryptic pocket detection, SWISH-X is out in JCIM & JCTC Journals! doi.org/10.1021/acs.jc… It combines SWISH's Hamiltonian replica exchange with expanded ensemble sampling with OPES to speed up cryptic pocket exploration. 1 / 🧵

New preprint! A synergistic combination of machine learning of collective variables with transition path sampling, with visiting PhD student Jintu Zhang arxiv.org/abs/2404.02597 #compchem #machinelearning #enhancedsampling (1/3)

Excited to share our new #preprint on #m6A's role in #RNA recognition! 🧬 A collaborative effort by Valerio Piomponi, Miroslav Krepl, Sponer lab, & Giovanni Bussi. Dive into our findings in this thread 👇

New paper out in The Journal of Chemical Physics with Thorben Fröhlking, Valerio Rizzi and Gervasio's Research Group (Protein Dynamics): learning path-like collective variables via a generalized autoencoder performing dimensionality reduction and continuous k-NN to tether the CV to training data pubs.aip.org/aip/jcp/articl… #ml #compchem

Luigi Bonati The Journal of Chemical Physics Thorben Fröhlking Valerio Rizzi Thrilled to announce our approach to learning path-like collective variables using a generalized autoencoder, now out in The Journal of Chemical Physics! This is the culmination of a journey that began with “From A to B in free energy space”. We get highly effective paths for enhanced sampling.

Our paper with Thorben Fröhlking Valerio Rizzi & Luigi Bonati on learning path-like collective variables with autoencoders is now out in The Journal of Chemical Physics ! This is the latest step in a journey that began with "From A to B in Free Energy Space". pubs.aip.org/aip/jcp/articl…

Excited to share my 1st independent preprint on data-efficient #ML potentials for catalytic & chemical reactions with Simone Perego💥 ➡️Uniformly accurate reactive MLPs with ~1k DFT calculations How❓Enhanced sampling + on-the-fly selection+ GNNs chemrxiv.org/engage/chemrxi… Short📜⤵️

Excited to see our work on accelerating DeepLNE++ published in The Journal of Chemical Physics at doi.org/10.1063/5.0226… The updated link for tutorials: github.com/ThorbenF/DeepL… Many thanks to Valerio Rizzi, Simone Aureli, and the entire Gervasio's Research Group (Protein Dynamics). Summary below: x.com/TFroehlking/st…

🚀Excited to share our #preprint on implementing constant pH metadynamics for #RNA oligomers! Check it out here: arxiv.org/abs/2410.16064. Thread 🧵:

MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data • MDRefine is a novel Python package that refines molecular dynamics (MD) simulation trajectories by integrating experimental data, improving alignment with observed molecular

🚀Introducing MDRefine: our new #python package for integrating experimental data with #moleculardynamics trajectories through diverse reweighting methods! Check out the #preprint: arxiv.org/abs/2411.07798. Summary in thread 🧵:

The corresponding News & Views from Gervasio's Research Group (Protein Dynamics), Thorben Fröhlking and Simone Aureli is now live! nature.com/articles/s4358… 🔓rdcu.be/exl41