Abstract
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.
Keywords: Structural bioinformatics, drug design, databases, molecular modeling, protein prediction servers
Current Bioinformatics
Title: Molecular Modeling Databases: A New Way in the Search of Protein Targets for Drug Development
Volume: 2 Issue: 1
Author(s): Nelson Jose Freitas da Silveira, Carlos Eduardo Bonalumi, Helen Andrade Arcuri and Walter Filgueira de Azevedo Junior
Affiliation:
Keywords: Structural bioinformatics, drug design, databases, molecular modeling, protein prediction servers
Abstract: 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.
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Cite this article as:
Jose Freitas da Silveira Nelson, Eduardo Bonalumi Carlos, Andrade Arcuri Helen and Filgueira de Azevedo Junior Walter, Molecular Modeling Databases: A New Way in the Search of Protein Targets for Drug Development, Current Bioinformatics 2007; 2 (1) . https://dx.doi.org/10.2174/157489307779314320
DOI https://dx.doi.org/10.2174/157489307779314320 |
Print ISSN 1574-8936 |
Publisher Name Bentham Science Publisher |
Online ISSN 2212-392X |
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