The main objective in a molecular docking problem is to find
an optimized conformation between the ligand (a rigid/flexible
small molecule), and the receptor, (a rigid/flexible macromolecule)
that results in a minimum binding energy.Two main works are calculating Solution encoding and Fitness function.it is nearly easy to create chromosome but I couldn't...I dont know is it possible to implementat this work with these algorithms in matlab environment? or I can change the source code of docking software.
The software I use for docking is Autodock & Autodock vina.
"I can change the source code of docking software."
Yes, You can change the code of the autodock software the accommodate your needs. The source code is freely available ,and comes with a GPL license. http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
I recommend going the code modification route. Less coding would be required, since you don't don't have to rewrite the entire framework.
Go to check the reference of Autodock, There's one explained the mechanism details of the genetic algorithm. I have that in my Zotero in the lab. I can't give you right now.
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