ADL: Vina questions: COM or Center, Search Space, Screening, and Source code

Qadri, Yawar yqadri at PHYSIOLOGY.UAB.EDU
Thu Jun 11 11:28:22 PDT 2009


I was playing with Vina and I had a few questions:
 
1. Am I inputting the geometric center or the center of mass of the receptor? I assume you mean the geometric center, but I keep reading COM, so I'd like to be sure.
 
2. For the size of the search space, should I account for the ligand size or is that irrelevant in the search algorithm? For larger ligands, is it necessary to add some buffer space? Is this equivalent to the grid size in AD?
 
3. When virtual screening, it seems that I'm wasting computational cycles recalculating things for each receptor/ligand pair when I assume some stuff could be maintained across the searches. I'm not sure though because the output isn't very verbose.
 
4. Will you be providing the source code? I'd like to look at the code and compile a 64-bit version.
 
Thanks.
 
YQ
 



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