Potential Drug Target Database

As its name has indicated, Potential Drug Target Database is the bioinformatics tool that focuses on either the known or potential drug targets. What is unique about this database compared to the others is that the drug target is visualized with its 3D structures.

Example is the search of acetylcholinesterase target as shown below and first target 1ACJ is selected:

Once clicked, it shows you the biochemical type, therapeutic area and the related disease that it can be treated. Target identification is important for modern drug discovery. When the target or receptor site is identified correctly, then only the proper protein-drug binding can occur and hence the therapeutic effects can work as stipulated.

The link attached when open will show the 3D-structure of the target molecule in particular its active sites, with this, the drugs with matching shape, size and configuration will bind to it. This tool is exceptionally useful in drug designing and it facilitates the fast and yet accurate inventions of new drugs.

National Center for Biotechnology Information Search database

National Center for Biotechnology Information Search database (NCBI) is a database that is used to determine the differences between the sequence of DNA and RNA. The NCBI is located in Bethaesda,Maryland and was founded in 1998.  

By searching Tamoxifen as an example, we can determine the sequence of the gene and the structure of the protein using the database called as National Center for Biotechnology Information Search Database (NCBI). Through this, the genetic codes of the protein, in which the specific amino acid it coded for can be identified. In some cases, the genetic disease can be identified and hence prevented.

On top of that, this database also enables the public to access most of the research studies to gather all the information that they required on the subject drugs or health issues. Examples are PubMed, MeSH and PubMed Central. Some of the full text articles that they provide are also free of charge which permits the quick and cost-saving means of accessing information from the students.

NCBI bookshelf offers cost free, downloadable biomedical e-books which contain various topics and a lot of information srelated to life science and healthcare. With the help of this e-book, researchers can have a wide and unlimited access to the endless pools of information. By this way, it not only helps to advance the information that one possess, but also able to contribute to the advancement in scientific field and research. 

NCBI is not only a database that store information but it also act as a platform to enable the users to share their latest results concurrently for the other users to review on it. This helps to boost the knowledge and enhance the quality of works from other researchers. Personally, I think that this database is very useful for us in doing research in future especially in our Year 4 Pharmacy studies.  

~~~ The RCSB Protein Data Bank ~~~

Figure 1

Figure 1 is about the website of Protein Data Base (PDB). 

      Now, I will introduce some information and the usage of this PDB website. For me, the PDB is something like your home's store, also know as repository. It can store a lot information about three-dimensional structure data of large biological molecules include proteins and nucleic acids in this database. 

      It is very useful for everyone especially for students and researchers to get knowledge from all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

     So, I will explain how to use and what we will get from here.

Figure 2

      First, we need to find something and type on this column which I mention (1). For example, we can type "Pepsin" to get information about the pepsin. Below Figure 3 is the information that we can get from this website.

Figure 3

      Now I will proceed to step 2 to click see what we will get.

Figure 4

      I think this is what we can get from this website ((( This is my FIRST time to log in here!!!!

Figure 5

      We can look the Crystal Structure and Proposed Amino Acid Sequence of A Pepsin from Atlantic Cod. We also can download this image to our devices for research, assignment and can use as profile picture too ((( Who will use this as profile picture????

Figure 6

      From step 3, we can know about the information of Pepsin deeply. From the molecular description, we can know the classification of Pepsin is Aspartyl Protease and the weight is 34033.80. ((( Where is the unit?? I just can confirm the unit is not in kg!!!!

Figure 7

      Now we can click here (4) to get more about the info.

Figure 8

      From this website, we also can obtain information such as molecular description that express the protein code of certain subject. This is useful for researchers to their studies and create product that produce therapeutic action against certain disease.

Figure 9

      In figure 10, we can get scientific name is Gadus morhua and common name is Atlantic Cod.

Figure 10

      In conclusion, Protein Data Bank store massive information systemically which make more efficient in searching information. By this way, I believe that this website can be useful for our research studies in future. That all is my explanation to introduce this website, Thank You for watching.

Therapeutic Targets Database

Some of the useful information about the known and unknown protein as well as the target for nucleic acid can be determined using a database called as Therapeutic Target Database. On top of that, with the use of this database, the targeted disease, information about the mechanism of the disease can be identified .

In this example, I am using the alzheimer's disease as the example.

There are some drug targets in which the drugs can act specifically to such as Acetylcholinesterase, NMDA receptor and many more. For example, Tacrine and Galantamine can act on the Acetylcholinesterase, Memantine can act on NMDA receptor. 

There are different levels of alzheimer's disease such as mild to moderate alzheimer's disease,cognitive impairment associated with the alzheimer's disease and tauopathies. In the mild to moderate alzheimer's disease, the drug targerts are amyloid beta and the drugs such as BAN2401 and UB-311 can act specifically to the drug target. In the cognitive impairment associated with the alzheimer's disease, 5-HT4 is the drug target in which the TD-8954 can act on this target drug. In the tauopathies, microtubule is the drug target in which the BMS-241027 can act specifically on a specific drug target. 

With the aid of this database, scientist can determine a specific drug target easily. if any disease occurs, scientist can cure a certain disease by focusing on the drug target and determine which drug that is useful and can act specifically to the drug target. 

HumanCyc: Encyclopedia of Human Genes and Metabolism

      HumanCyc is a database that provides an encyclopedic reference on human metabolic pathways. This database allow the public to obtain any information that require for research studies. Until year 2004, HumanCyc already contains around 250 metabolic pathways found in humans. Following are guidelines to perform a search:

Step 1: Open up HumanCyc official website

Step 2: Key in the target word and perform searching

Step 3: Obtain the complete information

     HumanCyc is an example which shows the beneficial of implanting information technologies into research field by improve the efficiency of research studies. Besides that, HamanCyc also enable us to keep and manage our information accordingly which easier for the public to obtain the information their require.

DrugBank database

There are many databases available to facilitate the drug designs...Let me start the journey by introducing to you all the DrugBank database.

DrugBank database is a bioinformatic tool in which it consists the details or information about various drugs, ranging from chemical, pharmaceutical and pharmacological data. Also includes in it is the comprehensive drug targets in which each of the specific drug binds.

Now I will start the search on Paracetamol.....As shown in picture below, the outcome of the search shows the generic name of Paracetamol that is Acetaminophen..

On top of the page, we can see the targets, enzymes, transporters and biointeractions (shown with different colours) that concerns with acetaminophen. It aids the researchers by organizing the information in a systematic way to ease the searching process.

Scrolling down to the page, one can see a lot of information regarding the drugs. Examples are: prescription products, generic prescription products, over the counter (OTC) products, different brand name, respective brand ingredients, chemical name and so on!

Example in the section of OTC products, it shows the dosage form of the drugs available, strength, route of administration, labeller and when is the drug marketing start. It brings huge benefits to not only the scientist but also the healthcare provider. For example, it helps to avoid the possible medication errors such as overdose and under dose of drugs when the appropriate dose range is available there.

Here is the link for the website: http://www.drugbank.ca/

Drug Adverse Reaction Target

Drug Adverse Reaction Target

This is a well-known database for the search of drug adverse reaction target by Bioinformatics & Drug Design group [BIDD] is a research group based in Department of Pharmacy, Faculty of Science, National University of Singapore. It contains many information about known drug adverse reaction targets, functions and properties. Related references are also included inside.  (The website address is at the second title of my post, just click it^^)

Front page of the website

It have a few search categorizes, and if you don't understand the meaning of that categorizes just click "question mark book" beside the box. 

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