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

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 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.

Modelos de recuperação de informação e web semântica: a questão da relevância

Introduction: In the Web environment, there is a need for greater care with regard to the processing of descriptive and thematic information. The concern with the recovery of information in computer systems precedes the development of the first personal computers. Models of information retrieval have been and are today widely used in databases specific to a field whose scope is known. Objectives: Verify how the issue of relevance is treated in the main computer models of information retrieval and, especially, as the issue is addressed in the future of the Web, the called Semantic Web. Methodology: Bibliographical research. Results: In the classical models studied here, it was realized that the main concern is retrieving documents whose description is closest to the search expression used by the user, which does not necessarily imply that this really needs. In semantic retrieval is the use of ontologies, feature that extends the user's search for a wider range of possible relevant options. Conclusions: The relevance is a subjective judgment and inherent to the user, it will depend on the interaction with the system and especially the fact that he expects to recover in your search. Systems that are based on a model of relevance are not popular, because it requires greater interaction and depend on the user's disposal. The Semantic Web is so far the initiative more efficient in the case of information retrieval in the digital environment.