Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Spatial Motifs
Similar Methods
Point-Surface Hybrid Descriptions

Strictly speaking, hybrid point-surface descriptions and single-point local Structure descriptions cannot be classified as structural motif Methods, yet they share a great deal in common. Surface-based methods are covered in Chapter 7.

The Cavbase (Schmitt et al. 2002; Kuhn et al. 2006) and SiteEngine (Shulman-Peleg et al. 2004) programs describe binding sites as sets of pseudoatoms combined with associated surface patches. The pseudoatoms correspond to various surface-exposed functional groups, such as Hydrogen bond Donors or acceptors. Comparison involves searching for geometrically and physicochemically compatible sets of pseudoatoms, spatially aligning the structures based on these pseudoatoms, and subsequently scoring them using patch overlap and physicochemical similarity. Since the number of surface points typically far exceeds the number of pseudoatoms, the scoring process is relatively resource-intensive. The two methods differ in certain details regarding pseudoatom description, scoring Implementation, and matching strategies: Cavbase relies on clique detection, whereas SiteEngine employs geometric hashing. Cavbase and its associated site database are available as part of the commercial Relibase+ software package under a license from the Cambridge Crystallographic Data Centre. The SiteEngine web server (Shulman-Peleg et al. 2005) (Table 8.3) performs pairwise comparisons but does not support database searching. For non-commercial use, a Linux executable can be downloaded (Table 8.3).