Evaluation of a grid based molecular dynamics approach for polypeptide simulations (Articolo in rivista)

Type

• Prodotto della ricerca (Classe)
• Articolo in rivista (Classe)

Label

• Evaluation of a grid based molecular dynamics approach for polypeptide simulations (Articolo in rivista) (literal)

Anno

• 2007-01-01T00:00:00+01:00 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi

• 10.1109/TNB.2007.903483 (literal)

Alternative label

• Merelli, Ivan; Morra, Giulia; Milanesi, Luciano (2007)
  Evaluation of a grid based molecular dynamics approach for polypeptide simulations
  in IEEE transactions on nanobioscience
  (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

• Merelli, Ivan; Morra, Giulia; Milanesi, Luciano (literal)

Pagina inizio

• 229 (literal)

Pagina fine

• 234 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume

• 6 (literal)

Rivista

• IEEE transactions on nanobioscience (Rivista)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali

• 6 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroFascicolo

• 3 (literal)

Note

• ISI Web of Science (WOS) (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni

• Istituto Tecnologie Biomediche (ITB) Consiglio Nazionale delle Ricerche (CNR) (literal)

Titolo

• Evaluation of a grid based molecular dynamics approach for polypeptide simulations (literal)

Abstract

• Molecular dynamics is very important for biomedical research because it makes possible simulation of the behavior of a biological macromolecule in silico. However, molecular dynamics is computationally rather expensive: the simulation of some nanoseconds of dynamics for a large macromolecule such as a protein takes very long time, due to the high number of operations that are needed for solving the Newton's equations in the case of a system of thousands of atoms. In order to obtain biologically significant data, it is desirable to use high-performance computation resources to perform these simulations. Recently, a distributed computing approach based on replacing a single long simulation with many independent short trajectories has been introduced, which in many cases provides valuable results. This study concerns the development of an infrastructure to run molecular dynamics simulations on a grid platform in a distributed way. The implemented software allows the parallel submission of different simulations that are singularly short but together bring important biological information. Moreover, each simulation is divided into a chain of jobs to avoid data loss in case of system failure and to contain the dimension of each data transfer from the grid. The results confirm that the distributed approach on grid computing is particularly suitable for molecular dynamics simulations thanks to the elevated scalability. (literal)

Prodotto di

• Bioinformatica in Biomedicina (ME.P06.027.001) (Modulo)
• Applicazioni della Bioinformatica e Neuroinformatica al GRID computing (PM.P06.010.001) (Modulo)

Autore CNR

• GIULIA MORRA (Persona)
• LUCIANO MILANESI (Persona)
• IVAN MERELLI (Unità di personale esterno)

Insieme di parole chiave

• Parole chiave di "Evaluation of a grid based molecular dynamics approach for polypeptide simulations" (Insieme di parole chiave)

Incoming links:

Autore CNR di

• LUCIANO MILANESI (Persona)
• IVAN MERELLI (Unità di personale esterno)
• GIULIA MORRA (Persona)

Prodotto

• Bioinformatica in Biomedicina (ME.P06.027.001) (Modulo)
• Applicazioni della Bioinformatica e Neuroinformatica al GRID computing (PM.P06.010.001) (Modulo)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#rivistaDi

• IEEE transactions on nanobioscience (Rivista)

Insieme di parole chiave di

• Parole chiave di "Evaluation of a grid based molecular dynamics approach for polypeptide simulations" (Insieme di parole chiave)