PPIDD: an extraction and visualisation method of biological protein-protein interfaces.
Biochimie
; 90(4): 640-7, 2008 Apr.
Article
em En
| MEDLINE
| ID: mdl-18086573
ABSTRACT
Today, the information for generating reliable protein-protein complex datasets is not directly accessible from PDB structures. Moreover, in X-ray protein structures, different types of contacts can be observed between proteins contacts in homodimers or inside heterocomplexes considered to be specific, and contacts induced by crystallogenesis processes, considered to be non-specific. However, none of the databases giving access to protein-protein complexes allows the crystallographic interfaces to be distinguished from the biological interfaces. For this reason we developed PPIDD (Protein-Protein Interface Description Database), an innovative tool, which allows the extraction and visualisation of biological protein-protein interfaces from an annotated subset of crystallographic structures of proteins. This tool is focused on the description of protein-protein interfaces corresponding to well-identified classes of protein assemblies. It permits the representation of any of these protein-protein assemblies (duplex) and their interfaces as well as the export of the corresponding molecular structures under a flexible format, which is an extension of the PDBML. Moreover, PPIDD facilitates the construction of subsets of interfaces presenting user-specified common characteristics, to enhance the understanding of the determinants of specific protein-protein interactions.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Conformação Proteica
/
Interface Usuário-Computador
/
Proteínas
/
Armazenamento e Recuperação da Informação
/
Bases de Dados de Proteínas
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Biochimie
Ano de publicação:
2008
Tipo de documento:
Article
País de afiliação:
França