Interaction of Chemical compound and Protein

4 posts / 0 new
Last post
sarakumar47
sarakumar47's picture
Interaction of Chemical compound and Protein

Hellow Everyone,
                   I have a drug and a protein. Earlier reports shows, the drug has capability to inhibit the action of that protein, but there was no detailed report regarding that, I mean where the drug bing to that protein, how it interacts, what is mechanism, etc. I wanna study those things. I don't have much (even not basic) knowledge about bioinformatcs, but If anyone tell me a best to study those things and which software shoud I use, I will learn everything and complete the study successfully. Please help me.
                   Sorry of not letting you know the name of drug and protein.
Saras

sps
sps's picture
Saras you are right in not

Saras you are right in not telling about the drug. But please do let us know if you want to study in vivo or directly you want to study the in vitro experimentation? As one must do the basic in vivo experimentation like X-ray crystallography and all so that you know about the structural properties of that proteina nad also the drug. The next step you can go with the bioinformatics tools. I will advice you to learn basic computer languages like C and C++, later you can go for MatLab. Learn this much after that you will be knowing thing on your own.

The FFM
The FFM's picture
do you know if your protein

do you know if your protein of interest has a crystal structure (PDB file) in the protein databases?
If so you can use Quantitative structure-activity relationships (QSAR) to investigate the binding and mechanism of block by the drug.
See these resources
http://www.netsci.org/Science/Compchem/feature12.html
www.qsarworld.com/
http://sourceforge.net/projects/qsar/
www.qsar.org/
www.ndsu.nodak.edu/qsar_soc/resource/software.htm
Publicly-accessible QSAR software tools developed by the Joint Research Centre

mishlabio
mishlabio's picture
Hi, if your protein of

Hi, if your protein of interest has a crystal structure in www.pdb.org, you can use it for performing docking studies. In case the structure is unavailable, homology modeling has to be done. Then proceed for docking.