How efficient surface representation can aid in bio-molecular simulation
INRIM, Edificio M
Istituto Italiano di Tecnologia, Genova
The progress of powerful experimental techniques such as Cryo-Electron Microscopy represents a remarkable opportunity but also a significant challenge for computational techniques, which aim at extracting useful information and predicting the behavior of biomolecular systems. While pioneering attempts to perform molecular dynamics simulation at this scale by means of supercomputers have been made, there still is the compelling need for enabling tools and approaches able to routinely analyze this kind of structures, identifying, for instance, interaction hot spots or new target regions for next generation drug discovery.
In this presentation I will describe the latest tool developments performed in my group in this direction, starting from the development of NanoShaper, a tool for building and analyzing the molecular surface of systems at the nanoscale, to its integration with the widely used VMD software utility.
Among the others, the possibility of interfacing NanoShaper with the DelPhi Poisson-Boltzmann equation (PBE) solver allows remarkable accuracy and robustness in the calculation of the electrostatic energy of large systems.
We are applying this computational toolkit to the analysis of MD trajectories and to the setup of ad hoc methods for accelerating the sampling of biomolecular events of pharmaceutical relevance.
Walter Rocchia graduated cum laude in Electronic Engineering on July 1996. In 2000, he got a PhD in Electronic Devices at the University of Trento. He then was a Research Scholar at the Biochemistry Department of the Columbia University, developing models to calculate the electrostatic field generated by biological macromolecules in solution.
In 2003 he joined the Molecular Biophysics group of National Enterprise for nanoScience and Nanotechnology (NEST-INFM-CNR), at Scuola Normale Superiore of Pisa, working on molecular recognition and targeting.
In 2008, he moved to the Drug Discovery and Development Department of the Italian Institute of Technology (IIT), working on computational approaches to ligand-protein binding free energy estimation.
In 2010 he was awarded, together with the Clemson University, a NIH 5-years grant entitled: DelPhi: Software for Electrostatic Modeling of Biomolecules and Objects.
In 2014, he created the Computational mOdelling of NanosCalE and bioPhysical sysTems (CONCEPT) Lab.
In 2014, he also co-founded BiKi Technologies, a spin-off company of IIT providing BioTech and Pharma companies with high-tech cutting-edge solutions mainly based on molecular dynamics and other advanced computational tools.
He is author of more than 70 publications including International Journals, book contributions and Proceedings.