Webinar: Finding a trade-off between speed and accuracy in protein-ligand binding description (2018-04-26)

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, 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 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. 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 ligandprotein
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. 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: https://attendee.gotowebinar.com/register/4351054872671182851
Webinar ID: 132-282-347


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