Ultrafast shape recognition

The basic idea of alignment-free shape matching is that a set of rotation- and translation-free descriptors are calculated for con-formers under consideration, and then some similarity measure is devised to quantify the similarity between two molecular objects. Zauhar s shape signatures (45), Breneman s PEST and PESD methods (54-56), the USR (ultrafast shape recognition) method... 

The USR (Ultrafast Shape Recognition) Method. This method was reported by Ballester and Richards (53) for compound database search on the basis of molecular shape similarity. It was reportedly capable of screening billions of compounds for similar shapes on a single computer. The method is based on the notion that the relative position of the atoms in a molecule is completely determined by inter-atomic distances. Instead of using all inter-atomic distances, USR uses a subset of distances, reducing the computational costs. Specifically, the distances between all atoms of a molecule to each of four strategic points are calculated. Each set of distances forms a distribution, and the three moments (mean, variance, and skewness) of the four distributions are calculated. Thus, for each molecule, 12 USR descriptors are calculated. The inverse of the translated and scaled Manhattan distance between two shape descriptors is used to measure the similarity between the two molecules. A value of 1 corresponds to maximum similarity and a value of 0 corresponds to minimum similarity. 

Ballester, P. J., Finn, P. W., Richards, W. G. (2009) Ultrafast shape recognition evaluating a new ligand-based virtual screening technology. J Mol Graph Model 27, 836-845. 

Ultrafast shape recognition (USR) [19] is a recent and unusually rapid descriptor-based shape similarity technique. USR is based on the observation that the shape of a molecule is determined by the relative positions of its atoms. This 3D spatial arrangement of atoms is accurately described by a set of distributions of interatomic distances measured from four strategically located reference points, which are in turn characterized by its first three statistical moments. The shape similarity of two molecules is Anally calculated through an inverse of the sum of least absolute differences in their respective descriptors (full details about this recent technique along with applications can be found in a recent review [20]). 

Ballester, P.J. and Richards, W.G. (2007) Ultrafast shape recognition for similarity search in molecular databases. Proceedings of the Royal Society A, 463, 1307-1321. 

Ballester, P.J. (2011) Ultrafast shape recognition method and applications. Future Medicinal Chemistry, 3 (1), 65-78. 

Zhou, X, Lafleur, K., and Caflisch, A. (2010) Complementing ultrafast shape recognition with an optical isomerism descriptor. Journal of Molecular Graphics ej Modelling, 29 (3), 443 49. 

Ballester, P.J. et al. (2010) Prospective virtual screening with ultrafast shape recognition the identification of novel inhibitors of arylamine N-acetyltransferases. Journal of the Royal Society Interface, 7 (43), 335—342. 

---