[Dock-fans] secondary scoring function

rafi A rafi4dd at gmail.com
Fri Jul 13 06:20:54 PDT 2007


Hello,

I am a new user of DOCK and i am having some basic questions.


I am interested to know about the secondary scoring function used for DOCK.
Particularly what is the secondary scoring function used frequently (or
found to be more useful)?.



>From the manual I understand that sec. scoring function is used in the final
minimization, scoring and ranking of molecules. I tried using grid scoring
for both primary and secondary scoring function. But the results in the
ranked files for primary and secondary scoring function are both same. In
this case should I attempt docking without using any secondary scoring
function.( rank_secondary_ligands: no).



Thanks in advance.



Best Regards,

Rafi
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