databases
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The University of Choice
CHAPTER 5
BIOINFORMATICS DATABASES
PHARMACY DATABASES
The University of Choice BIOLOGICAL DATABASE
• A biological database is a large, organized body
of persistent data, usually associated with
computerized software designed to update, query,
and retrieve components of the data stored within
the system.
• A simple database might be a single file containing
many records, each of which includes the same
set of information.
• For researchers to benefit from the data stored in a
database, two additional requirements must be met:easy
access to the information
a method for extracting only that information needed to
answer a specific biological question
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THERAPEUTIC TARGET DATABASES
• A database to provide information about the known and
explored therapeutic protein and nucleic acid targets,
• the targeted disease, pathway information and the
corresponding drugs directed at each of these targets.
• Also included in this database are links to relevant
databases containing information about target function,
sequence, 3D structure,
• ligand binding properties, enzyme nomenclature and
drug structure, therapeutic class, clinical development
status
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THERAPEUTIC TARGET DATABASES
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Statistics of this database
• This database currently contains 2,025 targets,
including 364 successful, 286 clinical trial, 44 discontinued
and 1,331 research targets, 17,816 drugs,
including 1,540 approved, 1,423 clinical
trial, 14,853 experimental drugs and 3,681 multi-target agents
(14,170 small molecules and 652 antisense drugs with
available strucuture or oligonucleotide sequence).
• Targets and drugs in this database cover 61 protein
biochemical class and 140 drug therapeutic classes
respectively.
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• The Therapeutically Relevant Multiple Pathways Database is designed to
provide information about such multiple pathways and related therpaeutic
targets described in the literatures, the targeted disease conditions, and the
corresponding drugs/ligands directed at each of these targets.
• This database currently contains 11 entries of multiple pathways, 97 entries of
individual pathways, 120 targets covering 72 disease conditions along with 120
sets of drugs directed at each of these targets.
• Each entry can be retrieved through multiple methods including multiple
pathway name, individual pathway name and disease name.
• Additional information provided include protein name, synonyms, Swissprot AC
number, species, gene name and location, protein sequence (AASEQ) and gene
sequence (NTSEQ) as well as potential therapeutic implications while
applicable.
• Cross-links to other databases are provided which include Genecard, GDB,
Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more
detailed information about various aspects of the particular target or non-target
protein.
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A database for facilitating the search for drug adverse reaction target. It
contains information about known drug adverse rection targets, functions
and properties. Associated references are also included.
The University of Choice DRUG POTENCY DATABASES
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Information of Drug Activity
Data • DPD is a relational database focusing on providing activity
information of drugs, clinical trial compounds and
experimental agents directed at their corrosponding
therapeutic targets.
• Also included in this database are links to relevant databases
containing information about target function, sequence, 3D
structure, ligand biding properties,
• enzyme nomenclature and drug structure, therapeutic class,
clinical development status.
• Currently this database contains 5000 records of activity for
around 3000 compounds direced at about 500 tagets.
Near 300 compounds in DPD have already approved or been
in the clinical trial stage.
The University of Choice POTENTIAL DRUG TARGET
DATABASE (PDTD)
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• PDTD is a dual function database that associates an
informatics database to a structural database of known
and potential drug targets.
• PDTD is a comprehensive, web-accessible database of
drug targets, and focuses on those drug targets with
known 3D-structures.
• PDTD contains 1207 entries covering 841 known and
potential drug targets with structures from the Protein
Data Bank (PDB).
• Drug targets of PDTD were categorized
into 15 and 13 types according to two criteria:
therapeutic areas and biochemical criteria.
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• The database supports extensive searching function
using PDB ID, target name and category, related
disease.
• Each record of drug target was prudently annotated by
hyperlinks to other databases, such as DrugBank, TTD,
ExPASy Proteomics Server and KEGG etc.
• In conclusion, PDTD serves as the cornerstone for
TarFisDock to identify the potential binding targets in-
silico
The University of Choice DRUGBANK
The University of Choice INTRO TO DRUGBANK
• The DrugBank database is a unique bioinformatics and cheminformatics
resource that combines detailed drug (i.e. chemical, pharmacological and
pharmaceutical) data with comprehensive drug target (i.e. sequence,
structure, and pathway) information.
• The database contains 6711 drug entries including 1447 FDA-approved
small molecule drugs, 131 FDA-approved biotech (protein/peptide) drugs,
85 nutraceuticals and 5080 experimental drugs.
• Additionally, 4227 non-redundant protein (i.e. drug
target/enzyme/transporter/carrier) sequences are linked to these drug
entries.
• Each DrugCard entry contains more than 150 data fields with half of the
information being devoted to drug/chemical data and the other half
devoted to drug target or protein data
The University of Choice BIOINFO DATABASE
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• HumanCyc is a bioinformatics database that describes
human metabolic pathways and the human genome.
• By presenting metabolic pathways as an organizing
framework for the human genome, HumanCyc provides
the user with an extended dimension for functional
analysis of Homo sapiens at the genomic level.
• For example, HumanCyc has tools for analysis of human
metabolomics and gene-expression data
The University of Choice PROTEIN DATABANK
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• The Protein Data Bank (PDB) archive is the single worldwide
repository of information about the 3D structures of large biological
molecules, including proteins and nucleic acids.
• These are the molecules of life that are found in all organisms
including bacteria, yeast, plants, flies, other animals, and humans.
• Understanding the shape of a molecule helps to understand how it
works.
• This knowledge can be used to help deduce a structure's role in
human health and disease, and in drug development.
• The structures in the archive range from tiny proteins and bits of
DNA to complex molecular machines like the ribosome.
• The PDB archive is available at no cost to users.
• The PDB archive is updated each week at the target time of
Wednesday 00:00 UTC (Coordinated Universal Time). The most
recent release is timestamped and linked on every page in the top
right header.
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• REF
• http://bidd.nus.edu.sg/group/cjttd/TTD_HO
ME.asp
• http://bidd.nus.edu.sg/group/ttd/ttd.asp
• http://bidd.nus.edu.sg/group/IDAD/IDAD_
Home.asp
• http://www.dddc.ac.cn/pdtd/index.php
• http://www.drugbank.ca/pharmabrowse/sm
all_molecule#subA10
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THANK YOU
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