BioExcel’s webinar series continue with a presentation from Walter Rocchia of BiKi Technologies



The continuous quest for better and more efficient tools for CADD, calls for methods
that are able to provide predictive results in limited time and computational resources.
In this context, I will present a few Molecular Dynamics based approaches that try to
extract useful practical information from MD simulations with relatively simple and
trivially parallel protocols.
In particular, I will focus on: i) the application of Scaled-MD for the ranking of
congeneric ligands based on residence time; ii) a specific bias accelerating the
dynamical docking of a ligand into the target binding site, and, iii) a tool for the
automated analysis of pocket dynamics along a MD trajectory.



Walter Rocchia

CONCEPT Lab (Computational mOdelling of NanosCalE and bioPhysical sysTems),
Italian Institute of Technology, Genoa, Italy

Biki Technologies (

Walter Rocchia graduated cum laude in Electronic Engineering on July 1996, with a
thesis on Quantum Computing. In February 2000, he got a PhD in Electroni c Devices at the University of Trento. He then was a Research Scholar at the Biochemistry Department of the Columbia University, developing models t o calculate the electrostatic field generated by biological macromolecules in solution. As a consultant in the Corporate Technology Centre at Honeywell Int (NJ, USA), and then at the Bioengineering Research Centre “E. Piaggio” of the University of Pisa he studied the modeling of the physical properties of actuating polymers and nanotubes in a wet environment. 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. There, he extended his interests from algorithms for speeding up and making more accurate the calculation of the electrostatic interaction energy of biomolecules to bioinformatic and biostatistical techniques aimed at identifying targets and engineering molecules involved in biochemical pathways of medical relevance. In 2008, he moved to the Drug Discovery and Development Department of the Italian Institute of Technology (IIT), working on computational approaches for ligandproteinbinding 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. He is author of more than 60 publications including International Journals, book contributions and
Proceedings, getting more than 2500 citations. 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.


Register for webinar

Title: Finding a trade-off between speed and accuracy in protein-ligand binding description

Date: 26th April, 2018
Time: 14:00 GMT / 15:00 CET

Registration URL:
Webinar ID: 132-282-347


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