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Protein-Ligand Docking in the New Millennium
tained using the original pocket coordinates and the default
scoring method.
Cross et al. [211] have also evaluated the performance of
DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex against
the DUD database. In particular, the authors found that
GLIDE (average AUC of 0.72) and Surflex (average AUC of
0.66) outperformed the other docking programs when used
for virtual screening (with average AUC values in the range
0.55 - 0.63).
CONCLUSIONS AND OUTLOOK
Over the past decade, protein-ligand docking has
emerged as a particular important tool in drug design and
development programs. This gain in standing is well por-
trayed in the rising number of available protein-ligand dock-
ing software programs, increasing level of sophistication of
its most recent applications, and growing number of users. In
spite of the large number of alternatives, we are still far from
a perfect docking program. In terms of the searching algo-
rithms, efficiently accounting for protein flexibility remains
a challenging task. In terms of the scoring functions features
like the presence of structural water molecules and the treat-
ment of entropy, among others, still pose considerable prob-
lems for protein-ligand docking. However, the high number
of programs, their geographically diverse origin, and the
different way in how they deal with the diverse challenges
posed by protein-ligand docking are all reasons that demon-
strate the vividness of the field.
Many protein-ligand docking programs are currently
available and new alternatives are continuing to appear every
year. Some of these alternatives will fade among the plethora
of protein-ligand docking applications, while others will rise
to become top choices among the users of the field. Given
the technical development pace in the field all alternatives
will eventually become obsolete, at least without a major
effort by the development teams in keeping their software
programs updated and competitive. Early adopters have the
major gain here, even though mastering a new software can
be difficult. The richness of this field is sure to make it worth
their effort.
CONFLICT OF INTEREST
The authors confirm that this article content has no con-
flicts of interest.
ACKNOWLEDGEMENTS
The authors would like to thank the financial support
provided by FCT (PTDC/QUI-QUI/100372/2008 and grant
no. Pest-C/EQB/LA0006/2011) and Fundação Calouste Gul-
benkian (Programa de Estímulo à Investigação 2009).
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