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DrugBank: a comprehensive resource for in silico
drug discovery and exploration
David S. Wishart*, Craig Knox, An Chi Guo, Savita Shrivastava, Murtaza Hassanali,
Paul Stothard, Zhan Chang and Jennifer Woolsey
Department of Computing Science and Department of Biological Sciences, University of Alberta, Edmonton,
AB, Canada T6G 2E8
Received August 14, 2005; Revised and Accepted October 8, 2005
ABSTRACT
DrugBank is a unique bioinformatics/cheminformat-
ics resource that combines detailed drug (i.e. chem-
ical) data with comprehensive drug target (i.e. protein)
information. The database contains .4100 drug ent-
ries including .800 FDA approved small molecule
and biotech drugs as well as .3200 experimental
drugs. Additionally, .14 000 protein or drug target
sequences are link ed 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 data-
bases (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 predic-
tion, drug interaction prediction and general pharma-
ceutical education. DrugBank is available at http://
redpoll.pharmacy.ualberta.ca/drugbank/.
INTRODUCTION
Until the 1980s, most of our knowledge about drugs, drug
mechanisms and drug receptors could fit in a few encyclope dic
books and a couple dozen schematic figures. However, with
the recent explosion in biological and chemical knowledge,
this is no longer the case. There is simply too much data
(images, models, structures and sequences) from too many
sources. Unfortunately, most of this information still resides
in textbooks or print journals. The limited drug or drug recep-
tor data that is electronically available is either inaccessible
(except through expensive subscriptions), inadequate or
widely scattered among many different public databases.
This state of affairs largely reflects the ‘two solitudes’ of
cheminformatics and bioinformatics. Neither discipline has
really tried to integrate with the other. As a consequence,
the wealth of electronic sequence/structure data that exists
today has never been well linked to the enormous body of
drug or chemical knowledge that has accumulated over the
past half century.
Recently, some notable efforts have been made to partially
overcome this ‘informatics gap’. The Therapeutic Target
Database or TTD is one such example (1). This very useful
web-based resource contains linked lists of names for >1100
small molecule drugs and drug targets (i.e. proteins). In addi-
tion to the TTD, a number of more comprehensive small
molecule databases have also emerged including KEGG
(2), ChEBI (3) and PubChem (http://pubchem.ncbi.nlm.nih.
gov/). Each contains tens of thousands of chemical
entries—including hundreds of small molecule drugs. All
three databases provide names, synonyms, images, structure
files and hyperlinks to other databases. Furthermore, both
KEGG and PubChem support structure similarity searches.
Unfortunately, these databases were not specifically designed
to be drug databases, and so they do not provide specific
pharmaceutical information or links to specific drug targets
(i.e. sequences). Furthermore, because thes e databases were
designed to be synoptic (containing <15 fields per compound
entry) they do not provide a comprehensive molecular sum-
mary of any given drug or its corresponding protein target.
More specialized drug databases such as PharmGKB (4) or on-
line pharmaceutical encyclopedias such as RxList (5) tend to
offer muc h more detailed clinical information about many
drugs (their pharmacology, metabolism and indications) but
they were not designed to contain structural, chemical or
physico-chemical information. Instead their data content is
targeted more towards pharmacists, physicians or consumers.
Ideally, what is needed is something that combines the
strengths of, say, PharmGKB, PubChem and Swiss-Prot to
*To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart@ualberta.ca
The Author 2006. Published by Oxford University Press. All rights reserved.
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D668–D672 Nucleic Acids Research, 2006, Vol. 34, Database issue
doi:10.1093/nar/gkj067
create a single, fully searchable in silico drug resource that
links sequence, structure and mechanistic data about drug
molecules (including biotech drugs) with sequence, structure
and mechanistic data about their drug targets. Beyond its obvi-
ous educational value, this kind of database could potentially
allow researchers to easily visualize and explore 3D drug
interactions, compare drug similarities or perform in silico
drug (or drug target) discovery. Here, we wish to describe
just such a database—called DrugBank.
DATABASE DESCRIPTION
Fundamentally, DrugBank is a dual purpose bioinformatics–
cheminformatics database with a strong focus on quantitative,
analytic or molecular-scale information about both drugs and
drug targets. In many respects it combines the data-rich
molecular biology content normally found in curated sequence
databases such as Swiss-Prot and UniProt (6) with the equally
rich data found in medicinal chemistry textbooks and chemical
reference handbooks. By bringing these two disparate types of
information together into one unified and freely available
resource, we wanted to allow educators and researchers
from diverse disciplines and backgrounds (academic, indus-
trial, clinical, non-clinical ) to conduct the type of in silico
learning and discovery that is now routine in the world of
genomics and proteomics.
The diversity of data types and the required breadth of
domain knowledge, combined with the fact that the data
were mostly ‘paper- bound’ made the assembly of DrugBank
both difficult and time-consuming. To compile, confirm and
validate this comprehensive collection of data, more than a
dozen textbooks, several hundred journal articles, nearly 30
different electronic databases, and at least 20 in-house or
web-based programs were individually searched, accessed,
compared, written or run over the course of four years. The
team of DrugBank archivists and annotators included two
accredited pharmacists, a physician and three bioinform-
aticians with dual training in computing science and molecular
biology/chemistry.
DrugBank currently contains >4100 drug entries, corres-
ponding to >12 000 different trade names and synonyms.
These drug entries were chosen according to the following
rules: the molecule must contain more than one type of atom,
be non-redundant, have a known chemical structure and be
identified as a drug or drug-like molecule by at least one
reputable data source. To facilitate more targeted research
and exploration, DrugBank is divided into four major categor-
ies: (i) FDA-approved small molecule drugs (>700 entries),
(ii) FDA-approved biotech (protein/peptide) drugs (>100 ent-
ries), (iii) nutraceuticals or micronutrients such as vitamins
and metabolites (>60 entries) and (iv) experimental drugs,
including unapproved drugs, de-listed drugs, illicit drugs,
enzyme inhibitors and potential toxins (3200 entries). These
individual ‘Drug Types’ are also bundled into two larger
categories including all FDA drugs (Approved Drugs) and
All Compounds (Experimental + FDA + nutraceuticals).
DrugBank’s cover age for non-trivial FDA-approved drugs
is 80% complete. In addition, >14 000 protein (i.e. drug
target) sequences are linked to these drug entries. More com-
plete information about the numbers of drugs, drug targets and
non-redundant drug targets (including their sequences) is
available in the DrugBank ‘download’ page. The entire data-
base, including text, sequence, structure and image data occu-
pies nearly 16 gigabytes of data—most of which can be freely
downloaded.
DrugBank is a fully searchable web-enabled resource with
many built-in tools and features for viewing, sorting and
extracting drug or drug target data. Detailed instructions on
where to locate and how to use these browsing/search tools
are provided on the DrugBank homepage. As with any web-
enabled database, DrugBank supports standard text queries
(through the text search box located on the home page). It
also offers general database browsing using the ‘Browse’ and
‘PharmaBrowse’ buttons located at the top of each DrugB ank
page. To facilitate general browsing, DrugBank is divided into
synoptic summary tables which, in turn, are linked to more
detailed ‘DrugCards’—in analogy to the very successful
GeneCards concept (7). All of DrugBank’s summary tables
can be rapidly browsed, sorted or reformatted (using up to six
different criteria) in a manner similar to the way PubMed
abstracts may be viewed. Clicking on the DrugCard button
found in the leftmost column of any given DrugBank summary
table opens a webpage describing the drug of interest in much
greater detail. Each DrugC ard 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
(see Table 1). In addition to providing comprehensive
numeric, sequence and textual data, each DrugCard also con-
tains hyperlinks to othe r databases, abstracts, digital images
and interactive applets for viewing molecular structures
(Figure 1). In addi tion to the general browsing features, Drug-
Bank also provides a more specialized ‘PharmBrowse’
feature. This is designed for pharmacists, physicians and
medicinal chemists who tend to think of drugs in clus ters
of indications or drug classes. This particular browsing tool
Table 1. Summary of the data fields or data types found in each DrugCard
Drug or compound information Drug target or receptor information
Generic name Target name
Brand name(s)/synonyms Target synonyms
IUPAC name Target protein sequence
Chemical structure/sequence Target no. of residues
Chemical formula Target molecular weight
PubChem/KEGG/ChEBI Links Target pI
Swiss-Prot/GenBank Links Target gene ontology
FDA/MSDS/RxList Links Target general function
Molecular weight Target specific function
Melting point Target pathways
Water solubility Target reactions
pKa or pI Target Pfam domains
LogP or hydrophobicity Target signal sequences
NMR/MS spectra Target transmembrane regions
MOL/SDF/PDF text files Target essentiality
MOL/PDB image files Target GenBank protein ID
SMILES string Target Swiss-Prot ID
Indication Target PDB ID
Pharmacology Target cellular location
Mechanism of action Target DNA sequence
Biotransformation/absorption Target chromosome location
Patient/physician information Target locus
Metabolizing enzymes Target SNPs/mutations
A more complete listing is provided on the DrugBank home page.
Nucleic Acids Research, 2006, Vol. 34, Database issue D669
Figure 1. A screenshot montage of the DrugBank Database showing several possible views of information describing the drug Ramipril. Not all fields are shown.
D670 Nucleic Acids Research, 2006, Vol. 34, Database issue
provides navigation hyperlinks to >70 drug classes, which in
turn list the FDA-approved drugs associated with the drugs.
Each drug name is then linked to its respective DrugCard.
A key distinguishing feature of DrugBank from other on-
line drug resources is its extensive support for higher level
database searching and selecting functions. In addition to the
data viewing and sorting features already described, Drug-
Bank also offers a local BLAST (8) search that supports
both single and multiple sequence queries, a boolean text
search [using GLIMPSE; (9)], a chemical structure search
utility and a relational data extraction tool (10). These can
all be accessed via the database navigation bar located at
the top of every DrugBank page.
The BLAST search (SeqSearch) is particularly useful as it
can potentially allow users to quickly and simply identify drug
leads from newly sequenced pathogens. Specifically, a new
sequence, a group of sequences or even an entire proteome can
be searched against DrugBank’s database of known drug target
sequences by pasting the FASTA formatted sequence (or
sequences) into the SeqSearch query box and pressing the
‘submit’ button. A significant hit reveals, through the associ-
ated DrugCard hyperlink, the name(s) or chemical structure(s)
of potential drug leads that may act on that query protein (or
proteome).
DrugBank’s structure similarity search tool (ChemQuery)
can be used in a similar manner to its sequence search tools.
Users may sketch (through ACD’s freely available chemical
sketching applet) or paste a SMILES string (11) of a possible
lead compound into the ChemQuery window. Submitting the
query launches a structure similarity search tool that looks for
common substructures from the query compound that match
DrugBank’s database of known drug or drug-like compounds.
High scoring hits are presented in a tabular format with hyper-
links to the corresponding DrugCards (which in turn links to
the protein target). The ChemQuery tool allows users to
quickly determine whether their compound of interest acts
on the desired protein target. This kind of chemical structure
search may also reveal whether the compound of interest may
unexpectedly interact with unintended protein targets. In addi-
tion to these structure similarity searches , the ChemQuery
utility also supports compound searches on the basis of chem-
ical formula and mol ecular weight ranges.
DrugBank’s data extraction utility (Data Extractor) employs
a simple relational database system that allows users to select
one or more data fields and to search for ranges, occurrences or
partial occurrences of words, strings or numbers. The data
extractor uses clickable web forms so that users may intuit-
ively construct SQL-like queries. Using a few mouse clicks, it
is relatively simple to construct very complex queries (‘find all
drugs less than 600 daltons with LogPs less than 3.2 that are
antihistamines’) or to build a series of highly customized
tables. The outpu t from these queries is provided as an
HTML format with hyperlinks to all associated DrugCards.
QUALITY ASSURANCE, COMPLETENESS
AND CURATION
Every effort is made to ensure that DrugBank is as complete,
correct and current as possible. Each DrugCard is entered or
prepared by one member of the curation team and separately
validated by second member of the curation team. Additional
spot checks are routinely performed on each entry by senior
members of the curation group, including a physician, an
accredited pharmacist and two PhD-level biochemists. Several
software packages including text mining tools, chemical para-
meter calculators and protein annotation tools (10) have been
modified or specifically developed to aid in DrugBank’s data
entry and data validation. These tools collate and display text
(and images) from multiple sources allowing the curators to
compare, assess, enter and correct drug or drug target informa-
tion. In addition to using a CVS (Current Versioning System),
all changes and edits to the central database are monitored,
dated and displayed on the DrugBank ‘download’ page using a
specially developed text tracking system. A second text track-
ing system has been implemented to monitor the completeness
(0–100%) of each field (for all approved drugs) and to display
up-to-date statistics on the number of drugs, drug targets and
non-redundant sequences in various drug categories. This
information is also displayed in the ‘download’ page. To
ensure DrugBank is current, new drugs (approved and experi-
mental) are identified using continuously running screen-
scraping tools linked to the FDA, the PDB and RxList web-
sites. Backfilling of older, more obscure and orphan drugs is
ongoing and done manually. Drug targets are iden tified and
confirmed using multiple sources (PubMed, TTD, FDA labels,
RxList, PharmGKB, textbooks) as are all drug structures
(KEGG, PubChem, images from FDA labels).
CONCLUSION
In summary, DrugBank is a comprehensive, web-accessible
database that brings together quantitative chemical, physical,
pharmaceutical and biological data about thousands of well-
studied drugs and drug targets. DrugBank is primarily focused
on providing the kind of detailed molecular data needed to
facilitate drug discovery and drug development. This includes
physical property data, structure and image files, pharmaco-
logical and physiological data about thous ands of drug pro-
ducts as well as extensive molecular biological information
about their corresponding drug targets. DrugBank is unique,
not only in the type of data it provides but also in the level of
integration and depth of coverage it achieves. In additio n to its
extensive small molecule drug coverage, DrugBank is cer-
tainly the only public database we are aware of that provides
any significant information about the 110+ approved biotech
drugs. DrugBank also supports an extensive array of visual-
izing, querying and search options including a structure sim-
ilarity search tool and an easy-to-use relational data extraction
system. It is hoped that DrugBank will serve as a useful
resource to not only members of the pharmaceutical research
community but to educators, students, clinicians and the
general public.
ACKNOWLEDGEMENTS
The authors wish to thank Genome Prairie, a division of
Genome Canada for financial support. Funding to pay the
Open Access publication charges for this article was provided
by Genome Canada.
Conflict of interest statement. None declared.
Nucleic Acids Research, 2006, Vol. 34, Database issue D671
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