Molecular Modeling Databases: A New Way in the Search of Protein Targets for Drug Development

Autor(es)

Jose Freitas da Silveira‚ N. ; Eduardo Bonalumi‚ C. ; Andrade Arcuri‚ H. ; Filgueira de Azevedo Junior‚ W.

• Tipo de documento: Artigo Científico
• Fonte: Current Bioinformatics; v. 2, n. 1, p. 1-10, 2007.

Resumo

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one step from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. (AU)

• Processo FAPESP: 99/12622-7 - Sementes: (1) regulação gênica da síntese de proteínas de reserva e metabolismo de lisina; (2) estudos de expressão de proteínas heterólogas
• Beneficiário: Daniele Beck Cardoso
• Modalidade de apoio: Bolsas no Brasil - Programa Capacitação - Treinamento Técnico
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