Software for optimizing drug molecules

From: jie liu

Dear All

 

I have a protein crystal structure with a bonded drug molecule. Before I proceed to serious and expensive computational approach, is there a free and simple software that I can use to do a little optimization of  the drug in order to enhance the bonding affinity, solubility and so on? I would like to have a general idea before going further.

 

Any input will be greatly appreciated. Have a good weekend!

 

Jie Liu

PHRI/NJMS/UMDNJ

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From: Hari Namboodiri

Dear Jie,

The best option for you is to download a trial version of commercial softwares like Maestro (Schrodinger), MOE (CCG) or Accelrys. Usually they give you a 30-day trial license during which time you can assess their feasibility.

Hope this helps.

Good Luck

Hari

Haridasan V. Namboodiri, Ph.D.

Episteme Biolabs

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From: jie liu

Dear Hari

 

Thank you so much. I will give it a try.

 

Best wishes

 

Jie

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From: Joel Tyndall

Dear Jie,

 

There isn't much that is free these days. Openeye offers "free" academic licenses but there is a clause in their agreement that they will claim license fees should the molecule become commercial.

 

Could you be a little bit more specific a about what type of optimization you are after? You can do a lot by "rational design" with just visualisation via say PyMOL.

 

Regards

 

Joel

 

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Joel Tyndall, PhD