SiteHopper - a unique tool for binding site comparison
© Batista et al; licensee Chemistry Central Ltd. 2014
Published: 11 March 2014
Knowledge of and information about protein binding sites has become increasingly important in the drug discovery process and not just for molecular biologists . By comparing binding sites within and across protein families, relevant details about the functionality and selectivity of a target protein can be extracted leading to useful insights for the development of new ligands . SiteHopper provides a powerful alternative method to the traditional use of sequence alignment for this purpose. Using OpenEye's Shape  and Spicoli toolkits , SiteHopper quickly calculates a 3D shape representation of the active site colored by the chemical properties of the protein residues defining the active site. These active site representations can be rapidly aligned and assessed for shape and chemistry similarity. As SiteHopper is built on the OpenEye toolkits, it is highly flexible and customizable for a variety of end-uses. In this presentation, the methodology behind SiteHopper will be introduced and multiple relevant applications will be shown.
- Paquet E, Viktor H: An exhaustive Shape-based approach for proteins' Secondary, Tertiary and Queaternary Structures Indexing, Retrieval and Docking. Prot Struct. 2012, 121-132.Google Scholar
- Binkowski T, Joachimiak A: Protein Functional Surfaces: Global Shape Matching and Local Spatial Alignments of Ligand Binding Sites. BMC Struct Biol. 2008, 8:Google Scholar
- Shape Toolkit 1.9.1: OpenEye Scientific Software, Santa Fe, NM. [http://www.eyesopen.com]
- Spicoli Toolkit 1.2.1: OpenEye Scientific Software, Santa Fe, NM. [http://www.eyesopen.com]
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.