- 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.
Onging research
Discovering proteins' cryptic pockets
CLC proteins - chloride channels and transporters
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:
Antimicrobial peptides
- 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:
Completed projects
Protein-ligand uninding protocol, that ranks ligands based on residence time
Protein-ligand unbinding protocol
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
Docking Guided by Adaptive Electrostatic Bias
Docking Guided by Adaptive Electrostatic Bias
A. Spitaleri, S. Decherchi, A. Cavalli and W. Rocchia; Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach. Journal of Chemical Theory and Computation 14(3) 2018
Dynamical characterization of water persistency in binding sites
Dynamical characterization of water persistency in binding sites
S. Rehana Zia, R. Gaspari, S. Decherchi and W. Rocchia. Probing Hydration Patterns in Class-A GPCRs via Biased MD: The A2A Receptor. Journal of Chemical Theory and Computation, 12(12), 2016