Previously (Hähnke et al., J Comput Chem 2010, 31, 2810) we introduced the concept of nonlinear dimensionality reduction for canonization of two-dimensional layouts of molecular graphs as foundation for text-based similarity searching using our Pharmacophore Alignment Search Tool (PhAST), a ligand-based virtual screening method. Here we apply these methods to three-dimensional molecular conformations and investigate the impact of these additional degrees of freedom on virtual screening performance and assess differences in ranking behavior. Best-performing variants of PhAST are compared with 16 state-of-the-art screening methods with respect to significance estimates for differences in screening performance. We show that PhAST sorts new chemotypes on early ranks without sacrificing overall screening performance. We succeeded in combining PhAST with other virtual screening techniques by rank-based data fusion, significantly improving screening capabilities. We also present a parameterization of double dynamic programming for the problem of small molecule comparison, which allows for the calculation of structural similarity between compounds based on one-dimensional representations, opening the door to a holistic approach to molecule comparison based on textual representations. © 2011 Wiley Periodicals, Inc. J Comput Chem , 2011.