Databases: Therapeutic Target Database (TTD)

Therapeutic Target Databases (TTD)

Therapeutic target databases is a database which provided by Bioinformatics and Drug Design Group in National University of Singapore. This database set as a platform to the easy access of information about the known therapeutic protein and nucleic acid targets to the targeted disease, pathway information and the corresponding drugs directed at each of these targets.

Figure 1 : Shows the main page of Therapeutic Target Databases(TTD)

Users able to retrieve information from the databases based on specific search by drugs and targets by disease, drugs, targets, biomarkers and drug scaffolds. The database also provides customized search, target similarity search, drug similarity search, Quantitative Structure Activity Relationship (QSAR) models, target validation, multi target agents, drug combination and nature-derived drugs.

In the column of Drug Combination search, the database provides drug-combination data such as pharmacodynamically synergistic,addictive, and antagonist combinations and pharmacokinetically potentiative and reductive combination together with their mode of actions and combination mechanisms.

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 structure or oligonucleotide sequence). Targets and drugs in this database cover 61 protein biochemical class and 140 drug therapeutic classes respectively

This database also provides links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class and clinical development status.

Therapeutically Relevant Multiple Pathways Database

         Basically, a disease processes will often occur between protein in some different pathways. These different protein has been used for the separately for treating a particular diseases. In order to facilitate mechanistic study of the drugs actions and more comprehensive understanding between different target of the same disease, therapeutically relevant multiple pathways database is developed. Furthermore, these database also contain detail about non-target proteins and natural small molecule involved in these same pathways which may provide useful hint for searching new therapeutic targets. On the other hand, these information also facilitate the understanding of how therapeutic targets interact with other molecules in performing specific tasks. 

Figure 1: The above picture showing the homepage of the Therapeutically Relevant Multiple Pathways Database

       Additionally, these database contain about 11 entries of multiple pathways, 97 entries of individual pathway, 120 targets covering 72 diseases conditions together with 120 steps of drugs directed at each of the target. 

Figure 2 : The above picture showing lipid , carbohydrate metabolism in adipose tissue cells.

                Besides that,  an additional information also available in this database such as protein name, synonyms, Swissprot Ac number, species, gene name and location, protein sequence and gene sequence as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM and SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein.

                         

Databases: Drug Adverse Reaction Target database (DART)

DRUG ADVERSE REACTION TARGET DATABASE (DART)

1. An adverse drug reaction (ADR) is an unexpected or dangerous event caused by taking a medication. It may occur due to a single dose or prolonged administration of a drug or result from the combination of two or more drugs. It often caused by the interaction of a drug or its metabolites with specific protein targets important in normal cellular function. Knowledge about these targets is both important in facilitating the study of the mechanisms of adverse drug reaction and in new drug discovery. The Drug Adverse Reaction Database (DART) is intended to provide comprehensive information about adverse effect targets of drugs described in the literature.

2. 

   Figure 1: The image above shows the homepage of the DART which is the abbreviation of Drug Adverse Reaction Database.
   
   

   Furthermore, this database gives physiological function of each target, binding drugs, agonists or antagonists, activators or inhibitors, corresponding adverse effects, and type of adverse effects induced by drug binding to a target. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3-dimensional structure, function, and nomenclature of each target along with drug or ligand binding properties. The database currently contains entries for 147 adverse reaction targets and 89 potential targets. A total of 187 adverse reaction conditions, 257 drugs, and 1080 ligands known to bind to each of these targets are also currently described.

   
   

   

   
   

   

   
   

   Figure 2: The image shows the results obtained from Drug Adverse Reaction Target database (DART) after an entry of choline esterase as a target.

   
   

   For instance, the images above shows the results obtained from the search of choline esterase as the target. It allows users to input targets, potential targets, adverse reaction conditions, drugs and ligands as shown in the image above. Moreover, each entry can be retrieved through multiple search methods including target name, target physiological function, adverse effect, ligand name, and biological pathways.

   
   

   In nutshell, Drug Adverse Reaction Target database (DART) is a database used for for facilitating the search for drug adverse reaction target. This database contains information about known drug adverse reaction targets, functions and properties. It also includes the associated references. In short, it allows users to access information about the adverse reaction targets of drugs which enhances the new drug discovery.

   
   

DrugBank

Figure 1: The above image shows the homepage of the DrugBank database and the search box on the right top of webpage. 

                The DrugBank database is a comprehensive, freely accessible, online database which combines the information of the drugs and drug targets. In detailed, this database which known as both bioinformatic and a cheminformatics resource will give more information about drug on chemical, pharmacological and pharmaceutical with the compressive drug target either chemical, structure and pathway information.

          Besides that, DrugBank database contain about 7759 drug entries and 4282 non-redundant protein including the drug target, enzyme, transporter and carrier sequences are linked to these drug entries. It is widely used by drug industry, medicinal chemists, pharmacist,physicians, students and public to obtain detail on drug. 

          By entering the drug names in the search box, these database will generates a tabular synopsis of the Drugbank's contents. Next, the browse will allow the user to casually scroll through the database or re-sort the contents. In order to obtain a complete information, the user require to click on the given DrugCard Button.

Figure 2 : The above image showing the structure of the drugs.

   Figure 3 : The above image showing the description of the drugs such as mechanism of action, pharmacodynamics, absorption and volume of distribution.   

Figure 4 : The above image showing the list of manufacturer.

Figure 5: The above image showing the information of drug interaction which might occur when the drug taken with another medication. 

               
              Basically, DrugBank database will look alike the above images when the user find for more information about drug.
     

Potential Drug Target Database [PDTD]

Potential Drug Target Database [PDTD]

There many websites or web pages that allows a user to search for databases related to drugs databases, biological databases, bioinformatics databases and many more. One of the web page that provides such databases are the Potential Drug Target Database [PDTD]. The figure below illustrate the web page. 

Figure 1: PDTD page 

Potential Drug Target Database [PDTD] is a dual function database that relates an informatics database to a structural database of known and potential drug targets (PDTD, 2008). In context, PDTD is a complete, web-accessible database of drug targets, and focuses on those drug targets with known 3D structures. 

According to PDTD (2008), it contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB). Furthermore, the drug targets in this web page is categorized into 15 and 13 types based on two criteria which are the biochemical criteria and therapeutic areas.  

On the other hand, the database also allows to search information using PDB ID, target name and category, related disease. 

Figure 2: When user browse PDTD by two criteria

Figure 3: When users search PDTD 

Example on the usage of PDTD

Under "Browse PDTD", upon clicking "Therapeutics Areas", I choose to acquire about information related to inflammation. Therefore, I clicked on inflammation as shown below and it provided me with information with 26 targets. 

Figure 4: Information listed under therapeutics areas

Figure 5: Information related to inflammation with 26 targets

With this, I was able to obtain more detailed knowledge in regards to enzyme. For instance, as shown in the figure below, 1CQE is an enzyme used for inflammation to treat diseases like Cardiovascular diseases and many more as listed below.

 Figure 6: Example of ICQE 

Databases: HumanCyc Database

HUMANCYC DATABASE

Generally, a database is a data which is usually related with the computerized software that is designed mainly to update, query and to obtain contents of the data stored within the system. It provides the users with easy access to the information as well as helps the users to extract the important and needed information. There are many databases available for various aspects of search. HumanCyc database is one of the database which is being used to obtain informations about the human genome. 

Figure 1: The image shows the homepage of the HumanCyc database where a gene, protein, metabolite or pathway can be entered on right top in the search menu.

The image above shows the HumanCyc database homepage. Generally, HumanCyc database is a Bioinformatics database which describes human metabolic pathways and the human genome. This provides the user with an extended dimension for the analysis of Homo sapiens based on genomic level by presenting metabolic pathways as an organizing framework for the human genome. This computational pathway analysis allows users to understand the analysis of the human genome assigned human enzymes to assumed metabolic pathways. 

This database encloses complete genome sequence of Homo sapiens. Furthermore, data about the human genome from Ensembl, LocusLink and GenBank were all combined or merged carefully so that a minimally redundant human gene set is created which is to be served as an input to SRI's Pathologic software. This software generates the database and predicted Homo sapiens metabolic pathways from functional information contained in the genome's annotation.

Moreover, the resulting pathway and genome database (PGDB) includes information on 28,783 genes, the metabolic reactions and pathways they catalyze. For instance, pyruvate in inserted in the Quick Search box at the upper right to analyze the metabolic pathways and the data. The picture below shows the results for the search. 

Figure 2: The image above shows the results for pyruvate in terms of pathways and proteins.

Figure 3: The image above shows the analysis of pyruvate in terms of protein.

Figure 4: The image above shows the results for pyruvate that is entered in the HumanCyc database in terms of Gene Ontology. 

Figure 5: The image above shows the analysis of pyruvate that is obtained from the HumanCyc database in terms of compounds and reactions. 

The images above shows the results which are are obtained from the search using the HumanCyc Database. The results are shows in terms of pathways, proteins, gene ontology (biological process, molecular function, cellular component), compounds, reactions and EC numbers. By providing results or analysis for the search that is entered by the users, HumanCyc allows the users to understand and learn more on the human genome and metabolic pathways. 

Protein Database : RCSB Protein Data Bank

PROTEIN DATA BANK

                          Figure 1 : Shows the homepage picture of the Protein Data Bank (PDB)

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecule, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologist and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBi, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank.

 

The PDB  is a key resource in area of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, now require scientist to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived databases that categorize the data differently. For an example, both SCOP and CATH categorize structure according to type of the structure and assumed evolutionary relations.
 

 

         
      Figure 2: Shows the list of information provided for each and every topic regarding protein.

                       Figure 3 : Shows the screen-print of one of the information in the database.

The information that I find interesting in the Protein Data Bank  is regarding the bacteria. There is a term called Bacteriorhodopsin.It actually describes a compact molecular machine which will use the sunlight to pump the protons across the plasma membrane. It was actually built by a halophilic bacteria. Halophilic bacteria is also known as a "salt loving" bacteria.This compact molecular machine usually found in high-temperature brine pools.The main function of it is actually they will use the sunlight to pump the proton outwards across the membrane, whereby making the inside 10,000-fold more alkaline than the outside.Using another type of protein, ATP synthase, building much of the ATP that powers the cell, these protons are allowed to flow back inwards. Bacteriorhodopsin is made up of three  protein chains. It is found embedded in dense arrays in the membranes of the bacteria. At the heart of the each protein chain is a molecule of retinal, which is bound deep inside the protein and connected through a lysine amino acid.

By capturing of the light, the bacteriorhodopsin could build four different types of rhodopsins. Rhodopsin is also a pump that funnels chloride ions instead of protons. Apart from that it is also function as keeping the internal concentration of chloride at high that match the salty condition outside the ce

About Me-Arivalagi

Hey!!!!
I would like to introduce myself..... My name is Arivalagi.... My friend likes to call me ARI!!!! I am 23 years old and currently living at Shah Alam.


Besides that, I'm  pursuing my Bachelor In Pharmacy (Hons) in Management and Science University (MSU). Basically, I'm doing my second semester now and my final exams in one month time. After the exam, I will happily go for one month holiday and prepare my self to face second year. That's about me for now.... Hope will write more in future.... Bye!!!!

Myself : Subashini Nadaraja

Hello everyone!!! I'm Subashini Nadaraja. I'm 20 years old, still young !!! :P...and my hometown is in Kuala Lumpur. Basically I am studying for Bachelor's In Pharmacy at Management and Science University (MSU) which is located at Shah Alam.This is my first time in life using a blog..I find it interesting anyway ! So, lets share the information together to gain something new and interesting !!!! :D :P :) I would like to thank my lecturer, Mr.Ibrahim for teaching me to create and use a blog through the subject  Bioinfomatics For Pharmacy.

About myself - Nareeta

Hey there, so I was told to describe something about myself and here I am, expressing about myself. 

Firstly, my name is Nareeta Kaur. In connection to my name, I often get question like "Is it the same like the Japanese Airport?". So yeah, I always get compared with Japan's "Narita". Basically, I am 21 years old and I am from Petaling Jaya. 

Besides that, I am currently doing my Bachelor in Pharmacy (Hons) in Management and Science University [MSU] at Shah Alam. At the moment, I am doing my second semester and my finals is in another month; and after that, I will finally finish my first year.  

Furthermore, I am writing this blog due to one of the subjects in my second semester which is the Bioinformatics for Pharmacy. This subject had allowed me to broaden my horizon towards the information technology world. Consequently, one of the outcome of me learning this subject is what I am doing now, writing a blog. I finally had the opportunity to try something that I never thought I would do. 

Last but not least, I would like to thank my lecturer, Mr. Ibrahim for educating and assisting the students in creating this blog. Thank you... 

About me: R.Sivasankari

Hola! I'm R.Sivasankari, student at Management and Science University. I'm currently studying for Bachelor of Pharmacy semester two. I chose this course as I love chemistry as well as to deal or learn more about drugs and their interactions. I'm from Penang and staying away from home could be make us feel down or sad most of the times but all the fun and experiences in Management and Science University are the biggest distractions for feeling homesick. So, this clearly explains that I'm enjoying my life here in MSU Shah Alam and looking forward to make more wonderful memories together with course mates. That's all about me for now. Stay tuned! Have a good day. Sayonara!

Something about me.. @sHwARn33

hey everyone..
welcome to our blog..I'm ashwarnee from penang..and yah..this is my very first time being a blogger...basically i don't like writing..hahaha

I tried my very best to squeeze my brain to write something..
well..its pretty hard for a science students to write poetically using flowery and bombastic words..

I don't know where should i start from..maybe from my first cry..is on 15th july 19**..by god's grace, i'm awarded with loving family which i loves more than anything else in the world...Currently i'm persuing my bachelor of pharmacy in Management and Science University (MSU). With the God's will,i have successfully passed my semester 1 and now in semester 2. You could imagined how it would be if i say a university student life like. Apart from that, with supporting lecturers and friends as well not forgetting family ; anything is possible..i always believe the quote 'if there is will,there is always a way' which reminds me of my schooldays..

The journey of friendship that begins in MSU

There is more coming up next..
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Have a good day ahead..! :)