I have the protein structure and would like to design the small molecule compounds to interfere with the protein function. I know which pocket to target. Last time I was in medicinal chemistry was 10 years ago. Could you please advise on the new software which could do the job?
Hi Konstantin,
I recommend the following academic-free drug-design software packages:
http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ
https://www.chemaxon.com/
http://www.eyesopen.com/
If you have enough money, the following software package should be nice:
http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm
Hello Konstantin Byrgazov ,
Today, there are many software available for protein ligand interaction and binding mode prediction.
Accelary discovery studio, Glide module of Schrodinger, Sybyl X, Auto Dock.
All this software are best suited for this type of study.
one of the article for basics of Docking study
doi: 10.1016/j.ejps.2015.08.017
All the best
Hi Konstantin,
Since you already have the target protein and the information of the binding pocket, you could use autodock tools to model the small molecule into the defined pocket. Autodock allows you to define the binding pocket (grid description) in which you want the small molecule to bind. This greatly reduces the search space instead of using the conventional blind docking.
As for screening of small molecules for your target protein/pocket you can use virtual screening methods such as autodock vina. It docks a library of compounds to the pocket and ranks them based on binding energies.
Additionally, since you know the binding pocket, you could use that information to design a pharmacophore and then select small molecules accordingly for docking.
Hope this helps.
best, Richa
Hi Konstantin,
I am agree with Richa,
Firstly it is free available
Second, you can watch the tutorial video on YouTube.
Third, It has been widely used for the type of work your want to do.
finally, you don't need to pay any money and permission for use. It gives fairly best results.
Hope you gonna do whatever is necessary.
Best regards
Omprakash
Hi Konstantin,
If you're starting to learn MD and apply it in your research, then I would recommend an excellent tutorial from Justin Lemkul as provided in link 1 below. It may also be useful to read up on past questions asked by others that relate to yours (link 2)
To help in setting up your MD simulation, I think MDweb (see links 3 and 4 below) is great tool for that as it supports the major MD softwares such as Gromacs, Amber, and NAMD.
Hope this helps and good luck on your research endeavors.
Best regards,
Chanin
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
https://www.researchgate.net/profile/Justin_Lemkul/answers
http://mmb.irbbarcelona.org/MDWeb/
http://mmb.irbbarcelona.org/MDWeb/help.php?id=tutorial
Hello
CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio.
Good Luck.
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