Within this project we use enchanced sampling molecular dynamics to force opening of interesting regions in the proteins' conformational space. 

We are stimulating opening of the cryptic pockets by tweaking behavior of the water molecules.

Using combined computational and experimental approach we investigate the effects of mutations on the function of proteins affected in rare genetic diseases. 

Within the project, our group is involved in enhanced sampling MD simulations exploring the chloride permeation pathway, and developing software aimed at predicting the effects of CLC mutations.

Collaboration:​​​

 

 

Project funding:

 

 

 

Within the STOP-SPREAD Bad Bugs consortium, we conduct computational and experimental analyses of antibacterial peptides and small molecules interacting with bacterial membranes. We work at the interface of academia and industry, in collaboration between IIT and an industrial partner.

Collaboration:

Project funding:

 

We designed an unbinding protocol that ranks congeneric ligands based on their residence time in a given target binding site

Luca Mollica, Sergio Decherchi, Syeda Rehana Zia, Roberto Gaspari, Andrea Cavalli and Walter Rocchia; Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations. Scientific Reports 5, 2015 View

 

 

 

 

 

We developed a technique to perform fully flexible protein ligand dynamic docking, guided by adaptive electrostatic bias

Andrea Spitaleri, Sergio Decherchi, Andrea Cavalli and Walter Rocchia; Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach. Journal of Chemical Theory and Computation 14(3) 2018 View

 

 

We developed a a tool to dynamically characterize water persistency and “happiness” in binding sites.

Syeda Rehana Zia, Roberto Gaspari, Sergio Decherchi and Walter Rocchia. Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor. Journal of Chemical Theory and Computation, 12(12), 2016 View