Molecular modeling databases: A new way in the search of protein targets for drug development

dc.contributor.authorda Silveira, Nelson José Freitas
dc.contributor.authorBonalumi, Carlos Eduardo [UNESP]
dc.contributor.authorArcuri, Helen Andrade [UNESP]
dc.contributor.authorde Azevedo Jr., Walter Filgueira
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionPontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
dc.contributor.institutionFaculdade de Medicina de São José do Rio Preto (FAMERP)
dc.description.abstractDBMODELING 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 DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop 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. © 2007 Bentham Science Publishers Ltd.en
dc.description.affiliationPrograma de Pós-Graduação em Biofisica Molecular Departamento de Física UNESP, Sao Jose do Rio Preto, SP 15054-000
dc.description.affiliationFaculdade de Biociências PUCRS, Porto Alegre, RS 90619-900
dc.description.affiliationDepartamento de Biologia Molecular Faculdade de Medicina de São José do Rio Preto - FAMERP, Sao Jose do Rio Preto, SP 15090-000
dc.description.affiliationInstituto de Pesquisa e Desenvolvimento UNIVAP, Sao Jose dos Campos, SP 12244-000
dc.description.affiliationUnespPrograma de Pós-Graduação em Biofisica Molecular Departamento de Física UNESP, Sao Jose do Rio Preto, SP 15054-000
dc.identifier.citationCurrent Bioinformatics, v. 2, n. 1, p. 1-10, 2007.
dc.relation.ispartofCurrent Bioinformatics
dc.rights.accessRightsAcesso restrito
dc.subjectDrug design
dc.subjectMolecular modeling
dc.subjectProtein prediction servers
dc.subjectStructural bioinformatics
dc.subject3 phosphoshikimate 1 carboxyvinyltransferase inhibitor
dc.subjecttransferase inhibitor
dc.subjectunclassified drug
dc.subjectaccess to information
dc.subjectamino acid sequence
dc.subjectantibacterial activity
dc.subjectbacterial genome
dc.subjectclient server application
dc.subjectcomputer interface
dc.subjectcomputer prediction
dc.subjectcomputer program
dc.subjectcomputer simulation
dc.subjectdrug design
dc.subjectdrug research
dc.subjectdrug structure
dc.subjectdrug targeting
dc.subjectenzyme inhibition
dc.subjectmolecular model
dc.subjectMycobacterium tuberculosis
dc.subjectnucleotide sequence
dc.subjectpriority journal
dc.subjectprotein database
dc.subjectprotein structure
dc.subjectsequence homology
dc.subjectweb browser
dc.subjectXylella fastidiosa
dc.titleMolecular modeling databases: A new way in the search of protein targets for drug developmenten
unesp.campusUniversidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas, São José do Rio Pretopt