Structure Motivator is a desktop application for studying the range of structures represented by small three-dimensional protein motifs. It evolved from a simpler application — Motif Dihedralizer — which was originally written to give off-line access to the same motifs as in the Motivated Proteins web application. However this has been extended both to allow the user to refine further the motifs provided, and to make the refinement tools provided within the application available for structures originating from the user himself.
Structure Motivator presents a group of motifs as points in a plot of dihedral angles. In addition to φψ plots, there are also options to view side-chain χ1 angles and the dihedral angles bounding each peptide bond. The key feature of the application is the ability to make selections of motifs from these plots, interactively with the mouse cursor and/or on the basis of the presence or absence of specific residues within the motif. Details of selected residues may be displayed in a list, from which they may be visualized in the Jmol 3D protein-viewer. Selections may be exported to spreadsheet or reimported for further analysis, and print and graphics functions are available.
A description of Structure Motivator has been published in BMC Structural Biology (2012) 12:26.
Structure Motivator 2.6.1 (March 2019) is available for download. This version incorporates the extended subcategories of beta bulges. Also included is PreMotivator, which enables one to generate input files of user-specified motifs suitable for direct input into the application. Instructions are provided within Structure Motivator and PreMotivator, and a more extensive user’s manual in pdf format is included with the distributions and is also available separately. Files for additional motifs not included in the Structure Motivator application (including retired motifs from v. 2.5) can also be downloaded, together with demo files for PreMotivator.
Structure Motivator and PreMotivator require Java to be installed on your computer (not your web browser) in order to run. (The link out to view individual motifs in a web browser no longer requires the java browser plugin, which is being phased out.)
Bug reports, suggestions for improvements, and requests for other motifs are welcome. Please use the Feedback link on the Motivated Proteins home page.