Databases

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

The University of Choice .

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


THERAPEUTIC TARGET DATABASES


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.


• 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.


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


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)


• 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.

http://www.rcsb.org/pdb/index.html

http://www.rcsb.org/pdb/index.html


• 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

http://redpoll.pharmacy.ualberta.ca/drugbank/

http://bidd.nus.edu.sg/group/cjttd/

http://www.expasy.org/



http://www.genome.jp/kegg/

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


• 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


• 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.

The University of Choice NCBI


• 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

http://bidd.nus.edu.sg/group/ttd/ttd.asp

http://bidd.nus.edu.sg/group/IDAD/IDAD_Home.asp



http://www.drugbank.ca/pharmabrowse/small_molecule

http://www.drugbank.ca/pharmabrowse/small_molecule


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