Structure Motivator: A tool for exploring small three-dimensional elements in proteins

Structure Motivator is a standalone application with an embedded relational database of proteins that, as a starting point, can furnish the user with a palette of unclassified small peptides or a choice of pre-classified structural motifs. Alternatively the application accepts files of data generated externally. After loading, the structural elements are displayed as two-dimensional plots of dihedral angles (φ/ψ, φ/χ1 or in combination) for each residue, with visualization options to allow the conformation or amino acid composition at one residue to be viewed in the context of that at other residues. Interactive selections may then be made and structural subsets saved to file for further sub-classification or external analysis. The application has been applied both to classical motifs, such as the β-turn, and ‘non-motif’ structural elements, such as specific segments of helices.Structure Motivator allows structural biologists, whether or not they possess computational skills, to subject small structural elements in proteins to rapid interactive analysis that would otherwise require complex programming or database queries. Within a broad group of structural motifs, it facilitates the identification and separation of sub-classes with distinct stereochemical properties.Comparing the architecture of different proteins can provide insights into the principles of their formation and function. Where proteins are very similar it can be useful to superimpose and inspect their three-dimensional structures computationally [1]. Proteins with less overall similarity may still share a common arrangement of secondary-structure features, as exemplified by the CATH [2] and SCOP [3] classification schemata. Outside the regions of secondary structure one can identify smaller structural motifs such as the β-turn [4], generally ranging from three to six residues in length, and defined by specific residues having particular dihedral angles or arrangements of hydrogen bonds [5]. In our st