| Abstract: | ABSTRACT: BACKGROUND: Searching for structural motifs across known protein structures can be useful for identifying unrelated proteins with similar function and characterising secondary structures such as beta-sheets. This is infeasible using conventional sequence alignment because linear protein sequences do not contain spatial information. beta-residue motifs are beta-sheet substructures that can be represented as graphs and queried using existing graph indexing methods, however, these approaches are designed for general graphs that do not incorporate the inherent structural constraints of beta-sheets and require computationally-expensive filtering and verification procedures. 3D substructure search methods, on the other hand, allow beta-residue motifs to be queried in a three-dimensional context but at significant computational costs. RESULTS: We developed a new method for querying beta-residue motifs, called BetaSearch, which leverages the natural planar constraints of beta-sheets by indexing them as 2D matrices, thus avoiding much of the computational complexities involved with structural and graph querying. BetaSearch demonstrates faster filtering, verification, and overall query time than existing graph indexing approaches whilst producing comparable index sizes. Compared to 3D substructure search methods, BetaSearch achieves 33 and 240 times speedups over index-based and pairwise alignment-based approaches, respectively. Furthermore, we have presented case-studies to demonstrate its capability of motif matching in sequentially dissimilar proteins and described a method for using BetaSearch to predict beta-strand pairing. CONCLUSIONS: We have demonstrated that BetaSearch is a fast method for querying substructure motifs. The improvements in speed over existing approaches make it useful for efficiently performing high-volume exploratory querying of possible protein substructural motifs or conformations. BetaSearch was used to identify a nearly identical beta-residue motif between an entirely synthetic (Top7) and a naturally-occurring protein (Charcot-Leyden crystal protein), as well as identifying structural similarities between biotin-binding domains of avidin, streptavidin and the lipocalin gamma subunit of human C8. AVAILABILITY: The web-interface, source code, and datasets for BetaSearch can be accessed from http://www.csse.unimelb.edu.au/~hohkhkh1/betasearch. |
