DrugBank: a comprehensive resource for in silico drug discovery and exploration

Wishart, David S.; Knox, Craig; Guo, An Chi; Shrivastava, Savita; Hassanali, Murtaza; Stothard, Paul; Chang, Zhan; Woolsey, Jennifer

doi:10.1093/nar/gkj067

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DrugBank: a comprehensive resource for in silico drug discovery and exploration

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Author(s): David S. Wishart ^* , Craig Knox , An Chi Guo , Savita Shrivastava , Murtaza Hassanali , Paul Stothard , Zhan Chang , Jennifer Woolsey

Publication date (Electronic): 28 December 2005

Journal: Nucleic Acids Research

Publisher: Oxford University Press

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Abstract

DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14 000 protein or drug target sequences are linked to these drug entries. Each DrugCard entry contains >80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Many data fields are hyperlinked to other databases (KEGG, PubChem, ChEBI, PDB, Swiss-Prot and GenBank) and a variety of structure viewing applets. The database is fully searchable supporting extensive text, sequence, chemical structure and relational query searches. Potential applications of DrugBank include in silico drug target discovery, drug design, drug docking or screening, drug metabolism prediction, drug interaction prediction and general pharmaceutical education. DrugBank is available at http://redpoll.pharmacy.ualberta.ca/drugbank/.

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Most cited references 9

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TTD: Therapeutic Target Database.

X Chen (2002)

A number of proteins and nucleic acids have been explored as therapeutic targets. These targets are subjects of interest in different areas of biomedical and pharmaceutical research and in the development and evaluation of bioinformatics, molecular modeling, computer-aided drug design and analytical tools. A publicly accessible database that provides comprehensive information about these targets is therefore helpful to the relevant communities. The Therapeutic Target Database (TTD) is designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3D structure, function, nomenclature, drug/ligand binding properties, drug usage and effects, and related literature for each target. This database can be accessed at http://xin.cz3.nus.edu.sg/group/ttd/ttd.asp and it currently contains entries for 433 targets covering 125 disease conditions along with 809 drugs/ligands directed at each of these targets. Each entry can be retrieved through multiple methods including target name, disease name, drug/ligand name, drug/ligand function and drug therapeutic classification.

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PharmGKB: the Pharmacogenetics Knowledge Base.

Micheal Hewett, Diane E Oliver, Daniel L Rubin … (2002)

The Pharmacogenetics Knowledge Base (PharmGKB; http://www.pharmgkb.org/) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies. Tools to browse, query, download, submit, edit and process the information are available to registered research network members. A subset of the tools is publicly available. PharmGKB currently contains over 150 genes under study, 14 Coriell populations and a large ontology of pharmacogenetics concepts. The pharmacogenetic concepts and the experimental data are interconnected by a set of relations to form a knowledge base of information for pharmacogenetic researchers. The information in PharmGKB, and its associated tools for processing that information, are tailored for leading-edge pharmacogenetics research. The PharmGKB project was initiated in April 2000 and the first version of the knowledge base went online in February 2001.

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GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

D. Lancet, J Prilusky, M Rebhan … (1997)

Modern biology is shifting from the 'one gene one postdoc' approach to genomic analyses that include the simultaneous monitoring of thousands of genes. The importance of efficient access to concise and integrated biomedical information to support data analysis and decision making is therefore increasing rapidly, in both academic and industrial research. However, knowledge discovery in the widely scattered resources relevant for biomedical research is often a cumbersome and non-trivial task, one that requires a significant amount of training and effort. To develop a model for a new type of topic-specific overview resource that provides efficient access to distributed information, we designed a database called 'GeneCards'. It is a freely accessible Web resource that offers one hypertext 'card' for each of the more than 7000 human genes that currently have an approved gene symbol published by the HUGO/GDB nomenclature committee. The presented information aims at giving immediate insight into current knowledge about the respective gene, including a focus on its functions in health and disease. It is compiled by Perl scripts that automatically extract relevant information from several databases, including SWISS-PROT, OMIM, Genatlas and GDB. Analyses of the interactions of users with the Web interface of GeneCards triggered development of easy-to-scan displays optimized for human browsing. Also, we developed algorithms that offer 'ready-to-click' query reformulation support, to facilitate information retrieval and exploration. Many of the long-term users turn to GeneCards to quickly access information about the function of very large sets of genes, for example in the realm of large-scale expression studies using 'DNA chip' technology or two-dimensional protein electrophoresis. Freely available at http://bioinformatics.weizmann.ac.il/cards/ cards@bioinformatics.weizmann.ac.il

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Author and article information

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (publisher-id): Nucleic Acids Research

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: 01 January 2006

Publication date (Print): 01 January 2006

Publication date (Electronic): 28 December 2005

Volume: 34

Issue: Database issue

Pages: D668-D672

Affiliations

Department of Computing Science and Department of Biological Sciences, University of Alberta Edmonton, AB, Canada T6G 2E8

Author notes

^*To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart@ 123456ualberta.ca

Article

DOI: 10.1093/nar/gkj067

PMC ID: 1347430

PubMed ID: 16381955

SO-VID: ddad2545-9f3d-457a-9b92-893a5ad02993

License:

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@ 123456oxfordjournals.org

History

Date received : 14 August 2005

Date revision received : 08 October 2005

Date accepted : 08 October 2005

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DrugBank: a comprehensive resource for in silico drug discovery and exploration

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Abstract

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RNA drug delivery

Most cited references 9

TTD: Therapeutic Target Database.

PharmGKB: the Pharmacogenetics Knowledge Base.

GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

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