Welcome

Protein Dynamics group, led by Prof. Francesco Luigi Gervasio, focusses on the development of methods for biomolecular simulations with emphasis on enhanced sampling methods, as well as multiscale and coarse-grained models. The group crucially contributed to the development of methods for overcoming the timescale problem (metadynamics, parallel-tempering metadynamics, path collective variables, SWISH), which are widely used across different fields ranging from nanotechnology to biophysics.

We apply these methods to study a multitude of complex biophysical phenomena, including protein dynamics and folding, ligand binding, allosteric mechanisms, and modes of action of cancer-causing mutations. Our simulations have guided the design of several allosteric inhibitors that are now in pre-clinical development as anticancer drugs. Furthermore, we have a fruitful line of experimental research (NMR, SPR, mutagenesis) to validate the computational predictions, as well as active collaborations with pharmaceutical companies (Astra Zeneca, Evotec, Heptares, and UCB).

New paper on the effect of the E545K mutation on PI3Kα kinase

Here, we perform biased and unbiased molecular dynamics simulations of PI3Kα and uncover, for the first time, the free energy landscape of the E545K PI3Kα…

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New paper on computational methods to identify and characterize cryptic sites

Here, we review the recent contributions of mixed-solvent simulations, metadynamics, Markov state models, and other enhanced sampling methods to the field of cryptic site identification…

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New paper on the binding mechanism of retinol to CRBP-I and CRBP-II

Here, we unravel the binding mechanism of retitol to the two most abundant retinol-binding isoforms, CRBP-I and CRBP-II, using enhanced sampling molecular dynamics simulations and surface…

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