DRUG ADVERSE REACTION TARGET DATABASE

DRUG ADVERSE REACTION TARGET DATABASE

Knowledge about known ADR targets is acquired from literature searching, which can be time consuming and difficult particularly for those not working in specific field. Therefore, a publicly accessible database that provides comprehensive information about these targets provides a convenient and useful platform for obtaining relevant information. Drug Adverse Reaction Target (DART) database, which contains information about the literature-described known target related to adverse effect of drugs.

Let's search something in DART, for example 'esterase'.

The above is some enzymes related to esterase. When clicked on phosphodiesterase, below information are shown.

This database is very important in looking at adverse reaction of drugs to improve patient's quality of life.

POTENTIAL DRUG TARGET DATABASE

Here, I shared another one useful database that are widely used in world. It is a database that are provided by the Bioinformatics and Drug Design Group in National University of Singapore, which provides 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. 

Moreover, 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.

Here are the link that you may checkout :

http://www.dddc.ac.cn/pdtd/ 

From this database we can search the by just click the search buttons and then proceed to the target name, disease name and others that we wants to search.

Foe example, we search for the enzymes 'esterase', here is the result that you may find out :

Here are some of the video that explain more about this database that you may interested to dig more.

NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION

National Center for Biotechnology Information is a multi-discipilinary research group composed of computer scientist, molecular biologist, mathematicians, biochemist, research physicians and structural biologist concentrating on basic and applied research in computational molecular biology. These investigators has contributes to basic science and serve as wellspring of new methods for applied research activities. It provides various database and molecular search tools with support documentation for the resources. 

Through this, we can choose the type of database we want to search and the terms in the search box and it will show the results of the database we search.

Why we should choose NCBI ?

• The Entrez search of NCBI allows a search across all databases:  Genome, Gene, Protein, Nucleotide, even PubMed

• NCBI gives you real-time results for all searches

• NCBI’s multi-database management allows you to go from one database to another without having to re-enter your search terms

Links: http://www.ncbi.nlm.nih.gov/

DRUGBANK DATABASE

Want to reveal some of the database regarding the drugs? 

Here one of the interesting website of the database which is widely used is DrugBank.

Here are the link:

http://www.drugbank.ca/

 ;)

The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. the resources are combination of both bionformatics and cheminformatics.  DrugBank is widely used especially by the drug industry, medicinal chemists, pharmacists, physicians, students and the general public. Its extensive drug and drug-target data has enabled the discovery and repurposing of a number of existing drugs to treat rare and newly identified illnesses.

DATABASE

Want to reveal some of the database regarding the drugs? 

Here one of the interesting website of the database which is widely used is DrugBank.

Here are the link:

http://www.drugbank.ca/

 ;)

The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. the resources are combination of both bionformatics and cheminformatics.  DrugBank is widely used especially by the drug industry, medicinal chemists, pharmacist , physicians, students and the general public. Its extensive drug and drug-target data has enabled the discovery and repurposing of a number of existing drugs to treat rare and newly identified illnesses.

Through this database we can search straightly the drugs we want to find out for example phenytoin sodium which is an anticonvulsant drugs in details as shown below.  

Then, click the link of phenytoin for details.

Its shows the complete infromation such as the structure of the drugs, type of the drugs, decription, categories, taxonomy and many more. 

The mostly important and most people looking of the pharmacology, indication, pharmacodynamics, mechanism of action. Thus, this database provided a full decription of the drugs. This greatly expanded and improved version of the database included 1344 approved small molecule drugs and 123 biotech drugs as well as 3037 unique drug targets. Version 2.0 also included, for the first time, withdrawn drugs, extensive food-drug and drug-drug interactions as well as ADMET (absorption, distribution, metabolism, excretion and toxicity) parameters.

From all of these they are a lot of benefits and information that we can get through this database.

HUMANCYC DATABASE

Human Encyclopedia

Human metabolic pathways and human genome have been one of the biggest mysteries ever been discovered long time ago. Discovering is one thing that every scientists must perform, however for us, searching for the discoveries could be a new hectic pathway of life. Sigh.

Here's the solution.

This electronic encyclopedia provides us (Homo Sapiens) with tremendous tools of gene, proteins, genome, metabolic pathway and more! Moreover, HumanCyc is built the same way as BioCyc. Video below is an introductory link to BioCyc that introduces us to basic and advance features of Pathway Tools software in the context of BioCyc. 

Let's have a look some features in HumanCyc:

Above is different links to various subtopics related to Human Genome Database. As you can see, there were many websites that related to the database

Let's search something interesting for our works in HumanCyc. A key input 'glycolysis' is inserted in search tab.

Your result should look like this

Have a click on several link of your search results. For example, here's result of glycolysis pathway:

Certain enzymes in the glycolysis:

If you feel suddenly lost in the website, they provide user guide for you to help bring you to the right path.

Enjoy^^

PROTEIN DATA BANK (PDB)

PROTEIN  DATA BANK (PCB)

Protein Data Bank (PDB) is a database that allow users to view three dimensional structure of a certain biological molecule in a drug. The images are usually obtained from X-ray crystallography or NMR spectroscopy submitted by the biologist or chemist from around the world. This database is accessible with internet for anyone . For example, if a user type any drug name, the results will appear in a molecule structure together with full description such as molecular weight, classification and others in the summary session. This database also will provide information like 3D view, sequence, annotation and few others.

This an example when a user type paracetamol in the search engine at the website. There are 3 results that related to the topic searched.

When viewing one of the results, the summary will appear just like the picture below.

When viewing the 3D image, the protein structure will appear.

BIOINFORMATICS AND DRUG DESIGN GROUP

Bioinformatics and Drug Design Group or BIDD are the research group that are developing in computational methods, software tools and database for drug discovery, target discovery, protein function prediction modeling of biological system and biomarker discovery. The group are based in Department of Pharmacy, Faculty of Science, National University of Singapore.

The main goals of this database are:

• Development of Bioinformatics databases and software 
• ™Development of Computer-aided drug design methods and software
• Tool development and mechanistic study of traditional Chinese medicine 

Using this database we can search for Pharmainformatics Databases, Bionformatics databases and Herbinformatics databases.

In Pharmainformatics Databases, we can have many optional to search for the databases. For instance we can search for drugs and drug targets, drugs, biomarkers and drug scaffolds. Then we will get the information about the drugs and also the structure of the drug. For more detailed about the drug we can go to the drug info and it will explain more detailed about the therapeutic drug database. 

This database are useful as  they are main inverse docking method for drug target discovery, developed the popular therapeutic target database and they among World's first in exploring learning methods for protein prediction, ADME-Tox prediction, target discovery and multi target virtual screening.

Links: http://bidd.nus.edu.sg/group/bidd.htm

ALL ABOUT US

HOW WE MET

This is a blog we have created together. We are the first year students of pharmacy in MSU. After enduring first semester together, we came up with this memorable project to cherish our friendship. Through this blog, we want to share lifelong journey, through happiness and sadness, thick and thin, rise and fall TOGETHER.