PROTEIN DATABASE

 

Potential Drug Target Database (PDTD)

                                                               

Target identification is important for modern drug discovery. With the advances in the development of molecular docking, potential binding proteins may be discovered by docking a small molecule to a repository of proteins with the 3D structures. Now what docking means? It is a method which predicts the preferred orientation of one molecule to the second when bound to each other to form a stable complex. Knowledge of preferred orientation in turn may be used to predict the strength of association or binding affinity betwene two molecules using scoring functions.

To complete this task, a reverse docking program and a dug target database with 3D are necessary. A web server, TarFisDock (Target Fishing Docking) has been developed, which has been widely used by others. Recently, a protein target database or Potential Drug Database (PDTD) has been constructed and have integrated PDTD with TarFisDock. This combination aims to assist target identification and validation.

In short, PDTD is a web-accessible protein database for in silico target identification. It currently contains more than 1100 protein entries with 3D structures presented in the Protein Data bank. The data are extracted from literature and several online databases such as TTD, DrugBank and Thomson Pharma. The database covers diverse information of more than 830 known or potential drug targets, including protein and active sites structures in both PDB and mol2 formats, related disease and biological functions as well as associated regulating pathway. Each target is categorized by both nosology and biochemical function. PDTD supports keyword search function, such as PDB-ID, target name, , and disease name. Data set generated by PDTD can be viewed with the plug-in of molecular visualization  tools and also can be downloaded for free. Remarkably, PDTD is specially designed for target identification. In conjugation with TarFisDock, PDTD can be used to identify binding protein for small molecules. The results can be downloaded in the form mol2 file with the binding pose of the probe compound and a list of potential binding targets according to their ranking scores.

Below are the statistics of the (i) Distribution of targets by biochemical criteria and (ii) distribution of targets in therapeutics areas

HUMANCYC DATABASE

HumanCyc database

The Humancyc Pathway- Genome Database and Pathway Tools Software as Tools for imaging and analysing metabolomics data.

-The above database is relevant to the Beyond the genome (BTG) is 

a (PGDB) pathway genome database: HumanCyc

Drugbank database

DRUG BANK 
Open Data Drug & Drug Target Database

  

Drug bank Database

     Drug bank database is a very useful database which consists of details about drugs data and comprehensive drug target and related to drug action.

This database assists 'in silico' drug target discovery, drug design, drug docking, or screening, drug metabolism prediction, drug interaction prediction, and general pharmaceutical education.  

Chemically oriented drug databases are typically oriented towards 

•     medicinal chemists
•     biochemists  
•     molecular biologists

A screenshot montage of some of DrugBank's new or modified querying tools including ChemQuery, TextQuery and an example of the new generic text query output.

          Each drugCard entry now contains more than 100 data fields with half of the information being devoted to drug/chemical data and the other half devoted to pharamcological, pharamcogenomic and molecular biological data. A number of new data fields, including food-drug interactions, drug-drug interactions and experimental ADME data have been added in response to numerous user requests. 

THERAPEUTIC TARGET DATABASE

The picture on the left exhibit a database which provides useful information about the known and explored therapuetic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. This database also includes other relevent features such as the 3D structure of the drug. ligand binding properties and many more information which can be extracted by a single click of the mouse. I have chosen a particular disease to show how this database works. For example, Myocardial Infarction.

This is how it looks when i enter myocardial infarction into the search engine. This page shows its specific therapeutic target of drug of myocardial infarction disease.In order to know more about the drug which serves the the target and action site. you should click on the linked code of the drug " Tenecteplase " .                   

                                              

once you have clicked the link just now, you will come to this page which shows sufficient information of this particular drug. looking at the target bar, the target site for myocardial infarction is known as "Fibrin-specific tissue plasminogen" in order to gain the information on its mechanism and how the drug works on the target site, you would be able to see the reference link.



This is where it goes. the website of US National Library of Medicine National Institute of Health. This website provides a brief information on the interaction of the drug and target site of myocardial infection disease. You can repeat this process for any kind of disease or target site.

The Therapeutically Relevant Multiple Pathways Database

The Therapeutically Relevant Multiple Pathways Database

   To facilitate mechanistic study of drug actions and a more comprehensive understanding the relationship between different targets of the same disease, it is useful to develop a database of known therapeutically relevant multiple pathways (TRMPs). The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic 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.

This is the page that allows us to search the multiple pathways

Example of multiple pathway (Cardiovascular system related pathways)

   

  This database is very helpful as it provides information regarding multiple and single pathways along with related therapeutic targets, corresponding drugs/ligands, targeted disease conditions, constituent individual pathways, structural and functional information about each protein in the pathways. It also enable us to search for a disease along with its individual pathways. It gives us a clear picture about the disease and the sequences of the diseases. This is quite handy for the students, researchers and lecturers to find out details about the disease pathways. 

   For instance, I searched about cardiovascular system related pathways and it displays the pathways. The pathways are simple and nice to be read. Using different colours and arrows in the pathways causes the diagram attractive. Information such as protein names, synonyms, species, gene name and location, protein sequences and gene sequences. Information about these proteins and small molecules involved in these pathways also provides useful hint for searching new therapeutic targets.

Drug Adverse Reaction Target Database

An adverse drug reaction (ADR) is an injury caused by taking a medication. ADRs may occur following a single dose or prolonged administration of a drug or result from the combination of two or more drugs. The meaning of this expression differs from the meaning of "side effect", as this last expression might also imply that the effects can be beneficial.The study of ADRs is the concern of the field known as pharmacovigilance. An adverse drug event (ADE) refers to any injury occurring at the time a drug is used, whether or not it is identified as a cause of the injury. An ADR is a special type of ADE in which a causative relationship can be shown.

BIOINFORMATICS DATABASES

DRUG ADVERSE REACTION TARGET DATABASE

An adverse drug reaction (ADR) often results from 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 ADRs and in new drug discovery. It is also useful in the development and testing of rational drug design and safety evaluation tools. The Drug Adverse Reaction Database (DART) is intended to provide comprehensive information about adverse effect targets of drugs described in the literature. Moreover, proteins involved in adverse effect targets of chemicals not yet confirmed as ADR targets are also included as potential targets. This database gives physiological function of each target, binding drugs/agonists/antagonists/activators/inhibitors, IC(50) values of the inhibitors, corresponding adverse effects, and type of ADR 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/ligand binding properties, and related literature. The database currently contains entries for 147 ADR 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. Each entry can be retrieved through multiple search methods including target name, target physiological function, adverse effect, ligand name, and biological pathways. A special page is provided for contribution of new or additional information.

BIOINFORMATICS AND DRUG DESIGN GROUP WEBSITE

A Database for facilitating the search for drug adverse reaction target. We can  find information about known drug adverse reaction targets,functions and properties

How to search informations in this website?
1.Query Methods
Queries can be submitted by entering the required information in any one or combination of the three fields in the form. All searching fields are case insensitive. Wild character of '*' and '?' is supported. '*' here represent a string of any length, and '?' represent any one character.


2.Target Name:
This search field accept both complete and incomplete name of protein target. For example, to find "Choline esterase", you can type either the full name of "Choline esterase" or its imcomplete name. Using imcomplete name search, all entries satisfy the query will be return. Searching with "choline" or "choline*" will match "ACETYLCHOLINE MUSCARINIC RECEPTOR", "ACETYLCHOLINE NICOTINIC RECEPTOR", "CHOLINESTERASE", and "BUTYRYLCHOLINESTERASE"; and searching with "Cholin?sterase" will match only "CHOLINESTERASE".


3.EC/SwissProt AC:
This field is exact match field. You must type in the exact EC number of enzyme or SwissProt Acess number. Wild character of '*' and '?' are NOT supported here. For example, enter EC number '3.1.1.7' or SwissProt access number 'P22303'will match 'Choline esterase' exactly.


4.Physilogical Function:
This field use the same searching method as Target Name. The Database will return all the entries which include the query keyword in their physiological function text.


5.Adverse Effect:
This field use the same searching method as Target Name. The Database will return all the entries which include the query keyword in their physiological function text.


6.Ligand:
This field use the same searching method as Target Name. The Database will return all the entries which include the query keyword in their physiological function text.

7.Pathway:
This field use the same searching method as Target Name. The Database will return all the entries which include the query keyword in their physiological function text.

 

Detailed Information of Choline Esterase Enzyme from BIDD Website

Another example of target enzyme : Dihydrofolate reductase

Get to know Us #durga #puva #kayshini #priya #eshu #pavitra

From the left; Puvanesware, Kayshini, Priyasri, Eshwari, Durga Devi , Pavitra.

This picture was taken during the MSU Balloon Charity Run! Come on, don't be shy and try to spot us in this picture :)

Zombie us - Be afraid people! Muhahahaha!!  Kayshini is missing here :(

Let us start our blogging session by introducing each and every one of us. So, here we go!

First up, Priyasri. She's the admin of this group. This girl is very unpredictable. She looks very quiet but you should never get cheated - judging her by that. She's a jovial person and she's simply intelligent. She's very sporting and dare to do just anything! She's a die hard fan of a tamil actor called Simbhu. 

Now, a little something about Eshwari. She is 22 this year. Being the eldest in group, she's just too caring and responsible. She's creative and definitely a very good artist. Well, to make this girl happy, just drop by a restaurant and buy her some food. 

Next, about Kayshini. This girl is just too unique by every single thing she does. Let us elaborate one by one. I simply love the way she laughs and walks. She is a lifetime vegetarian girl who would like to keep herself simple and she's a family-orientated girl. That what makes her beautiful!

Pavitra, however, is the cutest girl in our group. This girl is just too active and she can just handle anything. She can cook very well and she's famous for her chicken briyani. She is talkative and is very noticeable. She has many admirers. 

Now, let's us know  Puvanesware. She's  friendly and she knows how to keep everyone happy. We can laugh all day long whenever she is around. She never fails to be there when we need help. She's a smart girl and is good in memorizing things. 

So, you can now guess who is actually writing out in this blog. Yes, it's me -Durga Devi.  There's nothing special if you are the one to write and praise about yourself, isn't? So, I'm just gonna leave it like this and let me be the mysterious puzzle piece in this group. 

Thank you! Hope to blog on pretty soon! Have a good day everyone! <3 :D