Hi I am dealing with the drug design softwares. I have a set of ligands which have to be docked and affinity rankings should be predicted against 2 targets. I need to find the scaffold for that ligands. Can anyone help me out to find the tools for scaffold hopping?
Hi,
The following web servers may help you:
1) 1-Click Scaffold Hop
https://mcule.com/apps/1-click-scaffold-hop/
2) wwLigCSRre
http://bioserv.rpbs.univ-paris-diderot.fr/services/wwLigCSRre/
3) e-LEA3D
http://chemoinfo.ipmc.cnrs.fr/eDESIGN/index.html
4) ChemMapper
http://lilab.ecust.edu.cn/chemmapper/help.html
5) SwissBioisostere
http://www.swissbioisostere.ch/index.html
Hi Yoshinobu Ishikawa , thank you very much. I will give a try with these tools.
Hi
DataWarrior is good software for this. It also has other tools that allow small molecules databases analyzing and an excellent help.
Best wishes
Try Schrodinger software. It has the tools but you have to learn it. If you need a quick fix, I suggest you stay away from it.
Hi Saranya,
If you do not want to spend any money, try DataWarrior. It is free and can decompose scaffolds for you. It can even give you a plot of activity vs components if you have experimental data and a good QSAR.
I would recommend a professional software as Schrodinger Small Molecule Suite if you are serious. They have great prices and can give you a 30-day free trial to run it. Be prepared to know something before asking for a license. Otherwise, it is a waste of your time.
Dear Saranya,
There are a couple of tools you can use. First, you have to have a library of compounds with activities. You take the data and manually enter them into the table of your compounds. After that, you go to the QSAR module and ask it to build a model based on your activity data. In the specifications, you have a poor choice of parameters but you can add some like R groups and then ask again to build a model.
Using this model, you can predict properties for new compounds. I personally construct a library, screen it for binding and do a quick MD simulation for the best compounds. It is much better than simple docking.
I would prefer you to go to DataWarrior and do the same using biological activity data. It is a much simpler program and you can learn it quickly. Schrodinger is complicated and you need training, in-person or from the web. YouTube has plenty of those videos and you can ask your rep to give you a link to their library. They also organize courses but the material is proprietary and you have to agree to their confidentiality terms if they give you a full course video.
W
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