Riccardo Capelli

This work has been carried out with an extremely talented PhD student, Bruno Stegani 🙏

We would be happy to get comments and/or suggestions on this work! 🤠

The key of the technique is the linear dependency between the applied force and the double-logarithm of the residence time of the ligand: we find a parallelism with the Gumbel distribution, which can be due by the fact that rMD is filtering the maximal thermal fluctuations of the system!

Our computational "guinea pig" is the benzamidine-trypsin complex, which was extensively studied for this kind of calculations. We initially set up some parameters using an implicit solvent model (multi-eGO), then applying it to an atomistic force field

Kinetic rates calculation via non-equilibrium dynamics This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrati...

New preprint on arXiv! We propose a new technique to compute kinetic rates using multiple independent non-equilibrium (ratchet&pawl MD) simulations!
We focused here on ligand unbinding kinetics, but this method can be applied to any situation where a reaction coordinate can be defined!

My first post on bluesky, about my participation in this amazing symposium at ACS Spring 2025!

Thanks to the organizers @barakhirshberg.bsky.social @giovannimpiccini.bsky.social for the amazing lineup and for inviting me!

I think you put in the list a Brasilian politician instead of me 😬🤣