Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.

ROCCHIA, W.; NESHICH, G.; Scuola Normale Superiore, Italy; GORAN NESHICH, CNPTIA.

Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.

Abstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding.

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Bibliographic Details
Main Authors:	ROCCHIA, W., NESHICH, G.
Other Authors:	Scuola Normale Superiore, Italy; GORAN NESHICH, CNPTIA.
Format:	Artigo de periódico biblioteca
Language:	English eng
Published:	2007-12-07
Subjects:	Bioinformática, Biomoléculas, Banco de dados, Electrostatic potential of biomolecules, Protein structure analysis, Sting, Proteína, Bioinformatics, Protein structure,
Online Access:	http://www.alice.cnptia.embrapa.br/alice/handle/doc/899
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id	dig-alice-doc-899
record_format	koha
spelling	dig-alice-doc-8992017-05-12T01:37:51Z Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures. ROCCHIA, W. NESHICH, G. Scuola Normale Superiore, Italy; GORAN NESHICH, CNPTIA. Bioinformática Biomoléculas Banco de dados Electrostatic potential of biomolecules Protein structure analysis Sting Proteína Bioinformatics Protein structure Abstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding. 2011-04-10T11:11:11Z 2011-04-10T11:11:11Z 2007-12-07 2007 2017-05-11T11:11:11Z Artigo de periódico Genetics and Molecular Research, v. 6, n. 4, p. 923-936, 2007. http://www.alice.cnptia.embrapa.br/alice/handle/doc/899 en eng openAccess
institution	EMBRAPA
collection	DSpace
country	Brasil
countrycode	BR
component	Bibliográfico
access	En linea
databasecode	dig-alice
tag	biblioteca
region	America del Sur
libraryname	Sistema de bibliotecas de EMBRAPA
language	English eng
topic	Bioinformática Biomoléculas Banco de dados Electrostatic potential of biomolecules Protein structure analysis Sting Proteína Bioinformatics Protein structure Bioinformática Biomoléculas Banco de dados Electrostatic potential of biomolecules Protein structure analysis Sting Proteína Bioinformatics Protein structure
spellingShingle	Bioinformática Biomoléculas Banco de dados Electrostatic potential of biomolecules Protein structure analysis Sting Proteína Bioinformatics Protein structure Bioinformática Biomoléculas Banco de dados Electrostatic potential of biomolecules Protein structure analysis Sting Proteína Bioinformatics Protein structure ROCCHIA, W. NESHICH, G. Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.
description	Abstract. STING and JavaProtein Dossier provide a collection of physical-chemical parameters, describing protein structure, stability, function, and interaction, considered one of the most comprehensive among the available protein databases of similar type. Particular attention in STING is paid to the electrostatic potential. It makes use of DelPhi, a well-known tool that calculates this physical-chemical quantity for biomolecules by solving the Poisson Boltzmann equation. In this paper, we describe a modification to the DelPhi program aimed at integrating it within the STING environment. We also outline how the "amino acid electrostatic potential" and the "surface amino acid electrostatic potential" are calculated (over all Protein Data Bank (PDB) content) and how the corresponding values are made searchable in STING_DB. In addition, we show that the STING and JavaProtein Dossier are also capable of providing these particular parameter values for the analysis of protein structures modeled in computers or being experimentally solved, but not yet deposited in the PDB. Furthermore, we compare the calculated electrostatic potential values obtained by using the earlier version of DelPhi and those by STING, for the biologically relevant case of lysozyme-antibody interaction. Finally, we describe the STING capacity to make queries (at both residue and atomic levels) across the whole PDB, by looking at a specific case where the electrostatic potential parameter plays a crucial role in terms of a particular protein function, such as ligand binding.
author2	Scuola Normale Superiore, Italy; GORAN NESHICH, CNPTIA.
author_facet	Scuola Normale Superiore, Italy; GORAN NESHICH, CNPTIA. ROCCHIA, W. NESHICH, G.
format	Artigo de periódico
topic_facet	Bioinformática Biomoléculas Banco de dados Electrostatic potential of biomolecules Protein structure analysis Sting Proteína Bioinformatics Protein structure
author	ROCCHIA, W. NESHICH, G.
author_sort	ROCCHIA, W.
title	Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.
title_short	Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.
title_full	Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.
title_fullStr	Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.
title_full_unstemmed	Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.
title_sort	electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all pdb protein structures.
publishDate	2007-12-07
url	http://www.alice.cnptia.embrapa.br/alice/handle/doc/899
work_keys_str_mv	AT rocchiaw electrostaticpotentialcalculationforbiomoleculescreatingadatabaseofprecalculatedvaluesreportedonaperresiduebasisforallpdbproteinstructures AT neshichg electrostaticpotentialcalculationforbiomoleculescreatingadatabaseofprecalculatedvaluesreportedonaperresiduebasisforallpdbproteinstructures
_version_	1756023468068962304

Electrostatic potential calculation for biomolecules - creating a database of pré-calculated values reported on a per residue basis for all PDB protein structures.

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