Università degli Studi di Cagliari
Folding and Molecular Recognition in the Petascale era
27 maggio 2011
Si comunica che nell’ambito del Programma Visiting Professor 2010, il cui Ente finanziatore è la Regione Autonoma della Sardegna,
Il Prof. Francesco Luigi Gervasio
head of Computational Biophysics,
Spanish National Cancer Research Center,
Madrid, Spain
terra un seminario dal titolo:
"Folding and Molecular Recognition in the Petascale era"
Venerdi 27 Maggio ore 14.30 Aula E
presso
Dipartimento di Fisica
Cittadella Universitaria Monserrato
Abstract
Molecular dynamics (MD) simulations are a valuable tool for studying
complex bio-molecular systems, providing an atomistic description of
their structure and dynamics. Unfortunately, its predictive power has
been limited by the complexity of the biomolecule free energy
landscape, which prevented exhaustive sampling by means of standard
MD. Recently the use of specialized hardware and distributed computing
platforms as well as the development of advanced sampling algorithms,
has significantly alleviated the timescale limitation.
Here we show how a combination of MD codes running on GPU machines and
computational methods developed to accelerate rare events [1-2] and
can be used to study the mode of action of a novel allosteric
inhibitor to the Fibroblast Growth Factor receptor and to draft a new
theory on the mechanism of osmo-protection of proteins.
1. D. Branduardi, F. L. Gervasio and M. Parrinello. Rare events in
molecular systems: From A to B in Free Energy Space J. Chem. Phys.,
2007,126, 054103,
2. A. Laio and F. L. Gervasio* Metadynamics: a method to simulate rare
events and reconstruct the free energy in biophysics, chemistry and
material science Rep. Prog. Phys. , 2008, 71, 126601 (22p).
complex bio-molecular systems, providing an atomistic description of
their structure and dynamics. Unfortunately, its predictive power has
been limited by the complexity of the biomolecule free energy
landscape, which prevented exhaustive sampling by means of standard
MD. Recently the use of specialized hardware and distributed computing
platforms as well as the development of advanced sampling algorithms,
has significantly alleviated the timescale limitation.
Here we show how a combination of MD codes running on GPU machines and
computational methods developed to accelerate rare events [1-2] and
can be used to study the mode of action of a novel allosteric
inhibitor to the Fibroblast Growth Factor receptor and to draft a new
theory on the mechanism of osmo-protection of proteins.
1. D. Branduardi, F. L. Gervasio and M. Parrinello. Rare events in
molecular systems: From A to B in Free Energy Space J. Chem. Phys.,
2007,126, 054103,
2. A. Laio and F. L. Gervasio* Metadynamics: a method to simulate rare
events and reconstruct the free energy in biophysics, chemistry and
material science Rep. Prog. Phys. , 2008, 71, 126601 (22p).