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:
- Faculdade de Biociências-PUCRS, Av. Ipiranga, 6681. Porto Alegre, RS 90619-900, Brazil.,Brazil
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.
Export Options
About this article
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 |

- Author Guidelines
- Editorial Policies
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Allegations from Whistleblowers
- Publishing Ethics and Rectitude
- Increase Visibility Of Your Article
- Archiving Policies
- Reviewer Guidelines
- Guest Editor Guidelines
- Board Recruitment Workflow
- Short Guide
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Announcements
- Forthcoming Thematic Issues
Related Articles
-
Phage Choice, Isolation, and Preparation for Phage Therapy
Current Pharmaceutical Biotechnology Synthesis, Characterization, Antimycobacterial and Anticancer Evaluation of New 1,2,4-Triazole Derivatives
Letters in Drug Design & Discovery Integration of Biological Data with Semantic Networks
Current Bioinformatics Potential Use of Dendritic Cells for Anti-Atherosclerotic Therapy
Current Pharmaceutical Design Significant Induction of Soluble TNFR2 Compared with TNFR1 in Serum Samples of HIV Patients with or without Antiretroviral Medication
Infectious Disorders - Drug Targets Patent Selection
Recent Patents on Biotechnology Synthesis, Biological Activity of Thiazolidinones Bearing Indoline Moiety and Isatin Based Hybrids
Mini-Reviews in Organic Chemistry Gene Therapy by Liver Transplantation and Single Stranded Oligonucleotides (SSOs) in Familial Amyloidotic Polyneuropathy (FAP)
Current Pharmacogenomics γ δ T Cell Modulation in Anticancer Treatment
Current Cancer Drug Targets Medicinal Chemistry of Drugs with Active Metabolites Following Conjugation
Mini-Reviews in Medicinal Chemistry Novel Antibacterial Agents: An Emergent Need to Win the Battle Against Infections
Mini-Reviews in Medicinal Chemistry Monoclonal Antibodies in Allergy; Updated Applications and Promising Trials
Recent Patents on Inflammation & Allergy Drug Discovery Detection of the Incidence of Infections and Acute Biochemical Changes in Diffused Large B-Cell Lymphoma Patients Treated with Cyclophosphamide, Doxorubicin, Vincristine and Prednisone (CHOP) with and without Rituximab
Current Drug Safety Development of Anti-Atherosclerosis Therapy Based on the Inflammatory and Proliferative Aspects of the Disease
Current Pharmaceutical Design Design of Fucoidan Functionalized - Iron Oxide Nanoparticles for Biomedical Applications
Current Drug Delivery Advanced in Silico Methods for the Development of Anti- Leishmaniasis and Anti-Trypanosomiasis Agents
Current Medicinal Chemistry Quinoline-3-carboxylate Derivatives: A New Hope as an Antiproliferative Agent
Anti-Cancer Agents in Medicinal Chemistry Apolipoprotein E Gene Variants of Alzheimer's Disease and Vascular Dementia Patients in a Community Population of Nanking
Medicinal Chemistry New Insights on the Xenobiotic-Sensing Nuclear Receptors in Liver Diseases – CAR and PXR-
Current Drug Metabolism The Common Mycobacterial Antigens and their Importance in the Treatment of Disease
Current Pharmaceutical Design