We introduce TOPS+ strings, a highly abstract string-based model of protein topology that 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/outgoing arcs and ligand arcs respectively; 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 TOPS+ strings 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. Read the TOPS+ strings model representation for more information here.
Here you can compare a protein domain against the TOPS+ Database of TOPS+ strings models corresponding to the CATH version 2.4 protein domains. Please note that, the TOPS+ comparison is currently available only for a subset of the CATH version 2.4 protein domains.
Try the similarty search by TOPS+ Comparison here.