Subject: CCL: Docking accuracy versus computational time, demonstrated examples ?

From: [email-masked]
Date: Wed, 15 Jan 2003 12:08:23 -0600

CCL,

        Does anyone have first-hand experience or know of published papers 
which discuss docking accuracy versus computational 
time (for adjustable parameters within the various docking programs)?

        For example, many docking programs have adjustable parameters that 
affect docking results including accuracy (ligand 
coordinate RMS error relative to the crystal structure) and average 
computational time to compute each pose.  Sometimes, the goal is to
quickly dock a large set of compounds and obtain a (reasonable) set of 
poses for each compound.  Sometimes, the goal is to dock a 
much smaller set of compounds with the greatest accuracy possible, even if 
it takes 30 min - 1 hr (or more) of CPU time per compound.
One must make goal-oriented choices of parameters such as grid size, 
conformational analysis, treatment of short-range and long-range
forces and interaction energies, etc.

        Regards,
        Jim Metz

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

[email-masked]