, 4:P59,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 01 May 2012

SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs

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Novel high-throughput experimental techniques produce a large amount of data on the 3D structure of proteins and their structural motifs. These motifs can be used as patterns in drug discovery [1], can help to understand the relationship between a protein’s structure and its function [2] and to classify proteins [3]. In order to extract as much information as possible from this data, new techniques and tools are necessary, and among them fast approaches to perform the multiple superimposition of large sets of protein structural motifs. We report here on the development of such a tool.

We have implemented our newly developed multiple superimposition methodology in the web application SiteBinder, which is able to process hundreds of protein structural motifs in a very short time and provides an intuitive and user-friendly interface. We also demonstrate the applicability of SiteBinder using three case studies, focused on biologically important protein motifs. In the first case study, we co