DDESC: Dragon database for exploration of sodium channels in human

BackgroundSodium channels are heteromultimeric, integral membrane proteins that belong to a superfamily of ion channels. The mutations in genes encoding for sodium channel proteins have been linked with several inherited genetic disorders such as febrile epilepsy, Brugada syndrome, ventricular fibrillation, long QT syndrome, or channelopathy associated insensitivity to pain. In spite of these significant effects that sodium channel proteins/genes could have on human health, there is no publicly available resource focused on sodium channels that would support exploration of the sodium channel related information.ResultsWe report here Dragon Database for Exploration of Sodium Channels in Human (DDESC), which provides comprehensive information related to sodium channels regarding different entities, such as "genes and proteins", "metabolites and enzymes", "toxins", "chemicals with pharmacological effects", "disease concepts", "human anatomy", "pathways and pathway reactions" and their potential links. DDESC is compiled based on text- and data-mining. It allows users to explore potential associations between different entities related to sodium channels in human, as well as to automatically generate novel hypotheses.ConclusionDDESC is first publicly available resource where the information related to sodium channels in human can be explored at different levels. This database is freely accessible for academic and non-profit users via the worldwide web http://apps.sanbi.ac.za/ddesc.

[1]  David S. Wishart,et al.  Nucleic Acids Research Polysearch: a Web-based Text Mining System for Extracting Relationships between Human Diseases, Genes, Mutations, Drugs Polysearch: a Web-based Text Mining System for Extracting Relationships between Human Diseases, Genes, Mutations, Drugs and Metabolites , 2008 .

[2]  K. Chou.  Prediction of human immunodeficiency virus protease cleavage sites in proteins. , 1996, Analytical biochemistry.

[3]  V. Bajic,et al.  Dragon Plant Biology Explorer. A Text-Mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists[w] , 2005, Plant Physiology.

[4]  Kuo-Chen Chou,et al.  Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS , 2003, Biochemical and Biophysical Research Communications.

[5]  K. Chou.  Structural bioinformatics and its impact to biomedical science. , 2004, Current medicinal chemistry.

[6]  Darrell R. Abernethy,et al.  International Union of Pharmacology: Approaches to the Nomenclature of Voltage-Gated Ion Channels , 2003, Pharmacological Reviews.

[7]  W. Catterall,et al.  From Ionic Currents to Molecular Mechanisms The Structure and Function of Voltage-Gated Sodium Channels , 2000, Neuron.

[8]  K. Chou,et al.  Unified QSAR approach to antimicrobials. Part 3: first multi-tasking QSAR model for input-coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. , 2008, Bioorganic & medicinal chemistry.

[9]  Kuo-Chen Chou,et al.  MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. , 2007, Biochemical and biophysical research communications.

[10]  A. Wilde,et al.  A single Na(+) channel mutation causing both long-QT and Brugada syndromes. , 1999, Circulation research.

[11]  Alfred L George,et al.  Inherited disorders of voltage-gated sodium channels. , 2005, The Journal of clinical investigation.

[12]  Kuo-Chen Chou,et al.  HIVcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins. , 2008, Analytical biochemistry.

[13]  Stephen G. Waxman,et al.  International Union of Pharmacology. XXXIX. Compendium of Voltage-Gated Ion Channels: Sodium Channels , 2003, Pharmacological Reviews.

[14]  Sulayman D. Dib-Hajj,et al.  From genes to pain: Nav1.7 and human pain disorders , 2007, Trends in Neurosciences.

[15]  Kuo-Chen Chou,et al.  Agaritine and its derivatives are potential inhibitors against HIV proteases. , 2007, Medicinal chemistry (Shariqah (United Arab Emirates)).

[16]  Kuo-Chen Chou,et al.  Multiple field three dimensional quantitative structure–activity relationship (MF‐3D‐QSAR) , 2008, J. Comput. Chem..

[17]  Timothy A. Miller,et al.  Correlating phenotype and genotype in the periodic paralyses , 2004, Neurology.

[18]  Kuo-Chen Chou,et al.  Molecular modeling studies of peptide drug candidates against SARS. , 2006, Medicinal chemistry (Shariqah (United Arab Emirates)).

[19]  Kuo-Chen Chou.  Insights from modeling three-dimensional structures of the human potassium and sodium channels. , 2004, Journal of proteome research.

[20]  Kuo-Chen Chou,et al.  Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points , 2004, J. Chem. Inf. Model..

[21]  Kuo-Chen Chou,et al.  Screening for new agonists against Alzheimer's disease. , 2007, Medicinal chemistry (Shariqah (United Arab Emirates)).

[22]  Kuo-Chen Chou,et al.  HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. , 2008, Bioorganic & medicinal chemistry.

[23]  K. Chou,et al.  Recent progress in protein subcellular location prediction. , 2007, Analytical biochemistry.

[24]  J. Chou,et al.  Structure and mechanism of the M2 proton channel of influenza A virus , 2008, Nature.

[25]  L. Weiss,et al.  Sodium channels SCN1A, SCN2A and SCN3A in familial autism , 2003, Molecular Psychiatry.

[26]  Kuo-Chen Chou,et al.  Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. , 2007, Biochemical and biophysical research communications.

[27]  Lourdes Santana,et al.  Proteomics, networks and connectivity indices , 2008, Proteomics.

[28]  Kuo-Chen Chou,et al.  Computational approach to drug design for oxazolidinones as antibacterial agents. , 2007, Medicinal chemistry (Shariqah (United Arab Emirates)).

[29]  K. Chou,et al.  Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms , 2008, Nature Protocols.

[30]  Arno Siebes,et al.  Data and text mining Combination of text-mining algorithms increases the performance , 2006 .

[31]  K. Chou,et al.  Signal-3L: A 3-layer approach for predicting signal peptides. , 2007, Biochemical and biophysical research communications.

[32]  K. Chou,et al.  A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. , 1993, The Journal of biological chemistry.

[33]  Kuo-Chen Chou,et al.  Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. , 2004, Biochemical and biophysical research communications.

[34]  K. Chou,et al.  Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design. , 2008, Current protein & peptide science.

[35]  G. Breithardt,et al.  Genetic basis and molecular mechanism for idiopathic ventricular fibrillation , 1998, Nature.

[36]  William A. Catterall,et al.  International Union of Pharmacology. XL. Compendium of Voltage-Gated Ion Channels: Calcium Channels , 2003, Pharmacological Reviews.

[37]  Steven Petrou,et al.  SCN1A mutations and epilepsy , 2005, Human mutation.

[38]  Kuo-Chen Chou,et al.  Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design. , 2008, Protein and peptide letters.

[39]  Vladimir B. Bajic,et al.  Database for exploration of functional context of genes implicated in ovarian cancer , 2008, Nucleic Acids Res..

[40]  K. Chou,et al.  EzyPred: a top-down approach for predicting enzyme functional classes and subclasses. , 2007, Biochemical and biophysical research communications.

[41]  S. Waxman.  Channel, neuronal and clinical function in sodium channelopathies: from genotype to phenotype , 2007, Nature Neuroscience.

[42]  Kuo-Chen Chou,et al.  Heuristic molecular lipophilicity potential (HMLP): A 2D‐QSAR study to LADH of molecular family pyrazole and derivatives , 2005, J. Comput. Chem..

[43]  S. Priori,et al.  Cardiac sodium channel mutations in patients with long QT syndrome, an inherited cardiac arrhythmia. , 1995, Human molecular genetics.

[44]  K. Chou,et al.  ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information. , 2008, Biochemical and biophysical research communications.

[45]  Vladimir B. Bajic,et al.  Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining , 2004, Nucleic Acids Res..