Allows for the multiple superimposition of large sets of protein structural motifs. SiteBinder performs a systematic search for the atom pairing that provides the best fit. During this search, the root-mean-square deviation (RMSD) values for all chemically relevant pairings are calculated by quaternion algebra. The number of evaluated pairings is markedly decreased by using protein data bank (PDB) annotations for atoms. This approach guarantees that the best fit will be found and can be applied even when sequence similarity is low or does not exist at all. SiteBinder is able to process up to thousands of protein structural motifs in a very short time, and provides an intuitive and user-friendly interface. This interface consists of three basic elements: the rendering view, the input panel, and the results panel. The input panel includes the list of motifs and the selection tree. SiteBinder is freely available online.
National Centre for Biomolecular Research, Faculty of Science and CEITEC - Central European Institute of Technology, Masaryk University Brno, Brno-Bohunice, Czech Republic; Centre of Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
SiteBinder funding source(s)
This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic (ME08008), the Czech Science foundation (GD301/09/H004), the Science Foundation Ireland Grant 08/IN.1/B1949 and by the European Community’s Seventh Framework Programme (CZ.1.05/1.1.00/02.0068) from the European Regional Development Fund, and by Brno City Municipality through the program Brno Ph.D. Talent.