At present, we are focusing our efforts along the following main directions:
- developing new algorithms to accelerate the simulation of processes of pharmaceutical and biological relevance, such as the interaction between proteins and drug candidates;
- improving the description of systems from the nanoscale to the mesoscale by means of continuum electrostatics and advanced implicit solvent methods, with particular attention devoted to the description and calculation of molecular surfaces;
- developing highly scalable machine learning methods for the analysis of large data produced by microsecond long molecular dynamics simulations.
- In 2019 awarded EU-PRACE project: "In silico design of anti-idiotypic antibodies as broad-spectrum vaccines of Dengue and Zika"; 19.7M hours on MARCONI@CINECA, Italy
- In 2019 awarded ISCRA B project: "Design of a protein mimicking a broadly neutralizing Dengue virus antigen"; 1.6M hours on MARCONI@CINECA, Italy
- In 2015: member of the FETOPEN-RIA-2015-1 European project: “Protein Sequencing Using Optical Single Molecule Real-Time Detection”(ProSeqO)
- In 2015 awarded EU-PRACE project: Hydra; 68M hours on BGQ@CINECA, Italy
- In 2013: MOST-MAE bilateral Italy-Israel grant (as PI) “A comprehensive structure-based approach for identifying novel pathogen-specific drug targets"
- In 2010: 5-year NIH grant (as Co-Investigator) “DelPhi: Software for Electrostatic Modeling of Biomolecules and Objects”
- Miguel Machuqueiro's Group, Chemistry and Biochemistry Center, University of Lisbon - integrating continuum electrostatics modelling with Molecular Dynamics for constant-pH MD;
- Honig’s Lab (Columbia University, USA) - continuum electrostatics modelling, development and improvement of the Poisson-Boltzmann solver DelPhi;
- CNR-IMATI (ITA) - geometric aspects of molecular surfaces and data analysis;
- Kosloff Lab (ISRAEL) - a bilateral Italy-Israel grant is funding a shared project, aimed at finding new strategies against resistant pathogens.
Walter Rocchia is co-founder of BiKi Technologies, a spin-off of IIT incorporated in May 2014. BiKi comprises a multidisciplinary team of software engineers, computational chemists and biochemists working at the intersection of basic and applied research, providing pharmaceutical and biotech companies with innovative computational solutions. ( http://www.bikitech.com/)