12.16 STRIDE - Protein secondary structure assignment

12.16.1 Introduction

STRIDE is a well know software to recognize the protein secondary structure starting from atomic coordinates. It was developed by Dimitrij Frishman and Patrick Argos using the method explained in Frishman D., Argos P., "Knowledge-Based Protein Secondary Structure Assignment", Proteins: Structure, Function, and Genetics 23:566-579 (1995).
STRIDE plug-in interfaces VEGA ZZ to the original STRIDE code allowing to assign the secondary structure and to color the molecule by secondary structure.

12.16.2 Secondary structure table

To show the secondary structure table, you must select Calculate Stride Table in main menu:

Each table row defines a protein segment starting from the First to the Last residue placed in a specific Chain and Molecule. The secondary structure is indicated by the code (S) and the full description (Structure) as reported in the following table:

Selecting File Save menu item, you can save the table in CSV (Comma Separated Values) format in which the column order is preserved.

12.16.3 Secondary structure chart

To show the secondary structure pie chart, you must select Calculate Stride Table in the main menu:

Each sector illustrates the relative frequencies of the specific secondary structure type and their labels show the number of the residues classified inside them.

12.16.4 Color the molecule by secondary structure

To show the secondary structure pie chart, you must select View Color By structure in the main menu:

The structure is coloured using the following scheme:

12.16.5 Copyright

Original STRIDE copyright message:

All rights reserved, whether the whole or part of the program is concerned. Permission to use, copy, and modify this software and its documentation is granted for academic use, provided that:

1. this copyright notice appears in all copies of the software and related documentation;
2. the reference given below (Frishman and Argos, 1995) must be cited in any publication of scientific results based in part or completely on the use of the program;
3. bugs will be reported to the authors.

The use of the software in commercial activities is not allowed without a prior written commercial license agreement.

WARNING: STRIDE is provided "as-is" and without warranty of any kind, express, implied or otherwise, including without limitation any warranty of merchantability or fitness for a particular purpose. In no event will the authors be liable for any special, incidental, indirect or consequential damages of any kind, or any damages whatsoever resulting from loss of data or profits, whether or not advised of the possibility of damage, and on any theory of liability, arising out of or in connection with the use or performance of this software.

For calculation of the residue solvent accessible area the program NSC [3,4] is used and was kindly provided by Dr. F. Eisenhaber (EISENHABER@EMBL-HEIDELBERG.DE). Please direct to him all questions concerning specifically accessibility calculations.