The TOPStrings Protein Structure Comparison Method - A Novel Approach

Here, we introduce TOPStrings (TOPS+), a highly abstract string-based model of protein topology which permits efficient computation of structure comparison, and can optionally represent ligand information. In this model we consider loops as secondary structure elements (SSEs) as well as helices and strands; in addition we represent ligands as first class objects. Interactions between SSEs, and between SSEs and ligands are described by incoming and outgoing arcs, and SSEs are annotated with arc interaction direction and type. We are able to abstract away from the ligands themselves, to give a model characterized by a regular grammar rather than the context sensitive grammar of the original TOPS model (Gilbert, et al., 2000; Gilbert, et al., 2001; Viksna and Gilbert, 2001). Our TOPStrings model is sufficiently descriptive to obtain biologically meaningful results and has the advantage of permitting fast string-based structure matching and comparison as well as avoiding issues of NP-completeness associated with graph problems.