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

David P Leader* and E James Milner-White

Author Affiliations

College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK

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BMC Structural Biology 2012, 12:26  doi:10.1186/1472-6807-12-26

Published: 16 October 2012

Additional files

Additional file 1:

Schema of embedded database.The file shows those parts of the Protein Motif Database[5]retained in the embedded database in Structure Motivator.

Format: PDF Size: 243KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Statistical information and the anti-φψ plot.The file shows the anti-φψ plot for 2,3,-αRαR (5-residue) β-bulge loops. The points representing the combination of the ψ angle at position 2 and the φ angle at position 3 have been selected, and their mean values and the slope of the line through them is displayed in the statistics window of the console.

Format: PDF Size: 181KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Visualization of specific amino acids.The file shows the αL region at position 4 of a φψ plot of the type I β-turn. The three views shown are after console selection of gly as the ‘Highlighted Amino Acid’, with the respective options ‘include’, ‘exclude’ and ‘sole’. The selected amino acid, gly is coloured blue whereas other amino acids are coloured red.

Format: PDF Size: 119KB Download file

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Open Data

Additional file 4:

Visualizing amino acid composition and dihedral angles.The file shows the φψ plot at residue 4 of a type I β-turn. A pop-up listing the amino acid composition at this residue has been evoked by right-clicking within the plot, and a pop-up indicating the co-ordinates at the tip of the arrow cursor has been evoked by keeping it stationary for a few seconds.

Format: PDF Size: 162KB Download file

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Open Data

Additional file 5:

Structure Motivator Manual.The file contains a detailed description of the operation of Structure Motivator and PreMotivator.

Format: PDF Size: 1.7MB Download file

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Open Data