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

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da Silveira, Nelson José Freitas
Bonalumi, Carlos Eduardo [UNESP]
Arcuri, Helen Andrade [UNESP]
de Azevedo Jr., Walter Filgueira

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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 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.



Databases, Drug design, Molecular modeling, Protein prediction servers, Structural bioinformatics, 3 phosphoshikimate 1 carboxyvinyltransferase inhibitor, transferase inhibitor, unclassified drug, access to information, accuracy, amino acid sequence, antibacterial activity, automation, bacterial genome, bioinformatics, client server application, computer interface, computer prediction, computer program, computer simulation, drug design, drug research, drug structure, drug targeting, enzyme inhibition, human, Internet, molecular model, Mycobacterium tuberculosis, nonhuman, nucleotide sequence, priority journal, protein database, protein structure, review, sequence homology, web browser, Xylella fastidiosa

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Current Bioinformatics, v. 2, n. 1, p. 1-10, 2007.