Motif3D: Relating protein sequence motifs to 3D structure

Abstract

Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling fingerprint motifs of any of the receptors in this family to be mapped onto the single structure available, that of bovine rhodopsin. Motif3D can be used via the web interface available at: http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html.

Figure 1

Screen capture of the Motif3D input page available at http://www.bioinf.man.ac.uk/dbbrowser/motif3d/motif3d.html. The ‘Click here to try Motif3D’ link can be used to launch the viewer directly, with default parameters. The left hand form is used to launch Motif3D with a specific fingerprint ID and PDB code, if these are known. The right hand form provides a range of search facilities that allow users to enter a PDB code, fingerprint or sequence and find relevant structures and fingerprints with which to launch the viewer.

Figure 2

Screen capture showing results of launching Motif3D from a fingerprint entry. Clicking the ‘View Structure’ link at the top of the entry starts Motif3D with the motifs of the fingerprint (e.g. NEUROTENSINR) highlighted on an appropriate structure (e.g. 1F88). The accompanying web page provides instructions for use and other information about the program.