Wednesday, September 9, 2009

EasyQSAR: A beginners tool for QSAR in Drug Designing (Free software for drug designing and QSAR)

Computational chemistry represents molecular structures as a numerical models and simulates their behavior with the equations of quantum and classical physics. Available programs enable scientists to easily generate and present molecular data including geometries, energies and associated properties (electronic, spectroscopic and bulk). The usual paradigm for displaying and manipulating these data is a table in which compounds are defined by individual rows and molecular properties (or descriptors) are defined by the associated columns. A QSAR attempts to find consistent relationships between the variations in the values of molecular properties and the biological activity for a series of compounds so that these "rules" can be used to evaluate new chemical entities.
A QSAR generally takes the form of a linear equation
Biological Activity = Const + (C1 P1) + (C2 P2) + (C3 P3) + ...
where the parameters P1 through Pn are computed for each molecule in the series and the coefficients C1 through Cn are calculated by fitting variations in the parameters and the biological activity. Since these relationships are generally discovered through the application of advanced statistical techniques which might be very difficult to implement manually, so a tool that would do all this calculation and would be available freely would higly contribute to the field. I would not give a list of available tools available but would rather introduce you to a tool which has been developed by me. The main motivation behind developing the tool is to enable inexperienced users to get into the field and take up the work without any big pain to go through long tutorials.
EasyQSAR has a very friendly GUI that guides through every step and gives valuable tips to analyze the data. But one thing that should be remembered is that the tool only makes the analysis when you provide the data about the descriptors and activity. It does not generates the descriptors itself.
For any other query and troubleshoot
contact: kuntal.bhusan@gmail.com
To download visit : http://bioinformatikz.googlepages.com/
or, send a request mail to kuntal.bhusan@gmail.com





Step by step working instruction to perform a QSAR analysis using EasyQSAR

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  • A QSAR is of the form Biological Activity = Const + (C1 P1) + (C2 P2) + (C3 P3) + ... where the parameters P1 through Pn are computed for each molecule in the series and the coefficients C1 through Cn are calculated by fitting variations in the parameters and the biological activity.
  • NOW these P1,P2,P3 and so on are the descriptor variables of the QSAR equation you would be interested.
  • Many tools are available for generating these descriptors. Refer this link for calculating them : click here
  • Once you know how to calculate the descriptors the next thing which you need to get the possible other STRUCTURALLY RELATED drugs (by searching a drug library) and get their activity on the target.This is where you generate the library. Note: This library must be large enough (choose at least 10.
  • Calculate the descriptors(choose as many descriptors as you can and make sure that the descriptors you choose are varied enough ) for each compound from your library. (Also calculate the descriptors for your drug and keep it aside for now.) 
Prepare the input files as in the sample files ( You can test with the given sample files )
  • descriptor.csv : will contain the descriptor values for your library compounds
  • activity.csv : will contain the activity value for your library compounds 
    Replace the files with same name in the folder named QSAR generated automatically.

    • Now run the tool as per the instructions and generate the equation, the tool will guide you step by step for the analysis.
    • Choose "Analyze test data" option which will ask you to enter the descriptor values for an unknown sample (this is your drug). Enter the descriptor values in the .csv file in the same order as you entered for the library structures.This will predict the activity value for your drug compond based on the QSAR equation generated.


    To get a better idea you can have a look into these published works (links provided below) that used EasyQSAR for their work 


    1. Computational validation of 3-ammonio-3-(4-oxido- 1H-imidazol-1-ium-5-yl) propane-1, 1-bis (olate) as a potent anti-tubercular drug against mt-MetAP  click here
    2.  Synthesis, antimicrobial and QSAR studies of some new thiadiazepine derivatives click here
    3. Designing and screening of potent inhibitor against inha reductase of mycobacterium tuberculosis: a computational approach click here
    4. Molecular modeling and qsar analysis to explore therapeutic potentials of phytoestrogens in osteoporosis click here
    5. Resveratrol A Potent Angiotensin Converting Enzyme Inhibitor: A Computational Study in Relevance to Cardioprotective Activity. click here
    6. In-silico screening of potential inhibitors of gamma-secretase, a key enzyme of Alzheimer’s disease. click here
    7. Quantitative-Structure Activity Relationship (QSAR) Model for Abuse-liability Evaluation of Designer Drugs. click here
    8. Docking and QSAR based screening of some naturally occurring diterpenes as inhibitors of angiotensin converting enzyme (ACE) against cardiovascular diseases. click here
    9. An in silico insight into molecular mechanism of hypoglycemic activity of scoparic acid d, a diterpenoid from scoparia dulcis. click here




    Developed by:
    Kuntal Kumar Bhusan
    M.Tech Bioinformatics
    University of Hyderabad
    Post your queries and comments here.

    Reference to some of the content above is taken from :
    Introduction to QSAR Methodolog
    by AB Richon

    33 comments:

    1. Respected Sir,
      I am Monjur Ahmed Laskar I have done M.Sc in Bioinformatics from Jamia Millia Islamia in the Year 2009, Now I am a Trainee in the Bioinformatics centre, Assam University, Silchar,Assam,India.I am working in a project in which I have a unknown structure which has been isolated after Wet lab Experiment, what can I do with this structure with the help of Bioinformtics tools and sofrtware.Kindly suggest me.

      ReplyDelete
    2. you can make a structure profile search against the known databases and try to find out the nearest or related known structures to your protein..later you can validate it with some other descriptor properties...

      ReplyDelete
    3. Hi kuntal,
      even after filling registration form, i am clueless where to go to download EasyQSAR. please help me to download it..

      Best Wishes ,
      vamsi
      vamsi@nus.edu.sg

      ReplyDelete
    4. @vamsi
      After you complete the registration form you will get a link for the download page which you need to copy and paste in your browser link...

      ReplyDelete
    5. hello sir ,
      myself pammi shinde i'm doiing m.sc. in bioinformatics from davv indore. i've to make a presentation on QSAR but i don't know anything abut it can you explain what should i do?
      thank u

      ReplyDelete
    6. Where I can get EasyQSAR 1.0 software

      ReplyDelete
    7. hello sir i am thankful for your kind effort. i have downloaded the software but i am really not able to work with it.i am experiencing problem in learning the program even with the data set. so please give me a video guide or step wise demo of the software. my email id is
      avinashkumar.singh2010@vit.ac.in
      avinasahkumar1988@gmail.com

      ReplyDelete
      Replies
      1. Hai avinash kumar i am also facing the same problem what you are facing with EasyQSAR. Did you get the video guide or step wise demo regarding this. if so can u please send me to my id sadhu.shilpa@gmail.com

        Delete
    8. Hi Kuntal
      I appreciate your effort for starting this blog.
      As I don't have any access to commercial softwares for QSAR and I was searching for freeware for the same.I came accross the EasyQSAR program, I would like to use this program and would like to know more about the program and the type of statistical analysis that could be done with it.Also I would like to know whether the results that I would obtain for QSAR is publishable.

      Thank You

      Dr. Prija Ponnan

      ReplyDelete
    9. How do i choose my descriptors and activity...what should be in the test file

      ReplyDelete
    10. Hi Kunal,
      i am finding difficulty in inputting the descriptor data. I am having some molecules with biological activity and i am supposed to give data for respective descriptor
      then how can i input various data for respective descriptor?
      i m clueless.....

      ReplyDelete
    11. hi kunal
      can you please tell me hw to do 3d qsar using your software.

      ReplyDelete
    12. pelase refer to this publication :

      http://www.bioinformation.net/008/97320630008875.htm

      ReplyDelete
    13. hi kuntal

      Please help me how can I download this software

      ReplyDelete
    14. hello sir i am thankful for your kind effort. i have downloaded the software but i am really not able to work with it.i am experiencing problem in learning the program even with the data set. so please give me a video guide or step wise demo of the software. my email id is
      niktadge@gmail.com

      ReplyDelete
    15. hello sir, this is Kannan. S, i am experiencing problem in learning the program. so please give me a video guide or step wise demo of the software. my email id is kannan.2910@gmail.com

      ReplyDelete
    16. This comment has been removed by a blog administrator.

      ReplyDelete
    17. Hy, dear is any one know how to prepare and upload files in easyQSAR...?

      ReplyDelete
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    25. Please tell me how to generate activity and descriptors.

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