Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution (Articolo in rivista)

Type

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

Label

• Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution (Articolo in rivista) (literal)

Anno

• 2013-01-01T00:00:00+01:00 (literal)

Alternative label

• Sergio Decherchi, Jose Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov and Walter Rocchia,* (2013)
  Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution
  in Communications in computational physics (Online); Global Science Press, Wanchai (Cina)
  (literal)

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

• Sergio Decherchi, Jose Colmenares, Chiara Eva Catalano, Michela Spagnuolo, Emil Alexov and Walter Rocchia,* (literal)

Pagina inizio

• 61 (literal)

Pagina fine

• 89 (literal)

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

• 13 (literal)

Rivista

• Communications in computational physics (Rivista)

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

• 1 (literal)

Note

• ISI Web of Science (WOS) (literal)
• Google Scholar (literal)
• Scopu (literal)

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

• Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy. Institute for AppliedMathematics and Information Technologies, National Research Council of Italy, Genoa, Italy. Department of Physics, Clemson University, Clemson, South Carolina, USA. (literal)

Titolo

• Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution (literal)

Abstract

• The definition of amolecular surfacewhich is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuummodeling of biomolecular systems aswell as in themolecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atompositions, and the agreementwith explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson- Boltzmann calculations with the DelPhi solver. The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view. (literal)

Editore

• Global Science Press (Editore)

Prodotto di

• Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" (IMATI) (Istituto)
• Modellazione, analisi e classificazione di forme 3D derivate da strutture molecolari (INT.P02.008.001) (Modulo)

Autore CNR

• MICHELA SPAGNUOLO (Unità di personale interno)
• CHIARA EVA CATALANO (Unità di personale interno)

Insieme di parole chiave

• Keywords of "Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution" (Insieme di parole chiave)

Incoming links:

Autore CNR di

• CHIARA EVA CATALANO (Unità di personale interno)
• MICHELA SPAGNUOLO (Unità di personale interno)

Prodotto

• Istituto di matematica applicata e tecnologie informatiche \"Enrico Magenes\" (IMATI) (Istituto)
• Modellazione, analisi e classificazione di forme 3D derivate da strutture molecolari (INT.P02.008.001) (Modulo)

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

• Communications in computational physics (Rivista)

Editore di

• Global Science Press (Editore)

Insieme di parole chiave di

• Keywords of "Between algorithm and model: different Molecular Surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution" (Insieme di parole chiave)