ci060134h_si_001.doc (229.5 kB)
Geometric Accuracy of Three-Dimensional Molecular Overlays
journal contribution
posted on 2006-09-25, 00:00 authored by Qi Chen, Richard E. Higgs, Michal ViethThis study examines the dependence of molecular alignment accuracy on a variety of factors including the
choice of molecular template, alignment method, conformational flexibility, and type of protein target. We
used eight test systems for which X-ray data on 145 ligand−protein complexes were available. The use of
X-ray structures allowed an unambiguous assignment of bioactive overlays for each compound set. The
alignment accuracy depended on multiple factors and ranged from 6% for flexible overlays to 73% for
X-ray rigid overlays, when the conformation of the template ligand came from X-ray structures. The
dependence of the overlay accuracy on the choice of templates and molecules to be aligned was found to
be the most significant factor in six and seven of the eight ligand−protein complex data sets, respectively.
While finding little preference for the overlay method, we observed that the introduction of molecule flexibility
resulted in a decrease of overlay accuracy in 50% of the cases. We derived rules to maximize the accuracy
of alignment, leading to a more than 2-fold improvement in accuracy (from 19% to 48%). The rules also
allowed the identification of compounds with a low (<5%) chance to be correctly aligned. Last, the accuracy
of the alignment derived without any utilization of X-ray conformers varied from <1% for the human
immunodeficiency virus data set to 53% for the trypsin data set. We found that the accuracy was directly
proportional to the product of the overlay accuracy from the templates in their bioactive conformations and
the chance of obtaining the correct bioactive conformation of the templates. This study generates a much
needed benchmark for the expectations of molecular alignment accuracy and shows appropriate usages and
best practices to maximize hypothesis generation success.