Poster #RP129
DBMODELING: A database of structural models of proteins
Nelson Jose Freitas da Silveira*, Carlos Eduardo Bonalumi*, Helen Andrade Arcuri*, Walter Filgueira de Azevedo Junior**
*UNESP, São José do Rio Preto, Brazil; **PUCRS, Porto Alegre, Brazil
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, Plasmodium falciparum, 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 via our interactive website at http://www.biocristalografia.df.ibilce.unesp.br/tools. The DBMODELING user interface provides user friendly menus. 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 two other homology model databases: SWISSMODEL and MODBASE. The main applications of these databases are described in the present work.
Funding agencies: CNPq and Fapesp.