[Dock-fans] DOCKing with different architectures?

Marshall Levesque mlevesqu at ucsd.edu
Tue Jul 15 20:28:47 PDT 2008

This may be a general question that applies to all of the DOCK software
suite, or only certain parts:
If one were to perform a screening of 100 small compounds (eg from ZINC)
using DOCK6 (grid energy and/or AMBER score) and the workload was split
between two different architectures (32-bit/64-bit, different compiler
versions), are there any issues with using the results ranked by energy
score?  For this described situation, 50 compounds screened on each machine,
same target, same input files/parameters.

I'm asking this because if I run the same set of compounds on two different
architectures, I get similar results with similar rankings and scores, but
sometimes there is the occasional swing in score for some of the compounds
(eg -20 --> -8 for grid energy score).  These large changes in score are
obviously discomforting, but even the small changes (-20 --> -19) could
cause a significant shift in rankings when screen large datasets on the
order of 10^5 or 10^6.

Those most familiar with the DOCK algorithms might know best.  Is the
difference in score coming from different architectures something to do with
the calculation of the score? or the orientation/confirmation of the
compounds by anchor-and-grow?

I felt that the limited sampling of the search space results in the fact
that one can never produce a TRUE score, but more sampling does narrow the
window of discrepancy in energy score for the same compound DOCKed on two
different architectures, leading me to believe the conformation search is at

Any insight into this would be greatly appreciated, thanks!


UC San Diego Bioengineering
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