STRIDE Protein Secondary Structure Prediction

This is the original implementation of the STRIDE algorithm by Dmitrij Frishman as presented in:

• Frishman D, Argos P. Knowledge-Based Protein Secondary Structure Assignment Proteins: Structure, Function, and Genetics 23:566-579 (1995)

From the abstract, STRIDE calculates "protein secondary structure assignments form atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information"

This program also exists as a webservice at http://webclu.bio.wzw.tum.de/stride/.

This distribution also includes nsc by Frank Eisenhaber as presented in:

• F. Eisenhaber, P. Lijnzaad, P. Argos, M. Scharf "The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies" Journal of Computational Chemistry (1995) v.16, 273-284.

• F. Eisenhaber, P. Argos "Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency" Journal of Computational Chemistry (1993) v.14, N11, pp-1272-1280.

The nsc component calculates residue solvent accessible areas.

In 2013, the authors of STRIDE and nsc released the software under the terms of the MIT licence.

For more information on how to use stride, refer to doc/stride.doc

Purpose of the repository

This repository is originally a fork of https://github.com/josch/stride, and might be modified and updated to serve as the base STRIDE implementation for the ProteinSecondaryStructures.jl Julia package.

References

1. Frishman,D & Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.
2. Kabsch,W. & Sander,C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22: 2577-2637.
3. Eisenhaber, F. and Argos, P. (1993) Improved strategy in analytic surface calculation for molecular systems: handling of singularities and computational efficiency. J. comput. Chem. 14, 1272-1280.
4. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C., and Scharf, M. (1995) The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. comput. Chem. 16, 273-284.
5. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
6. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
7. Pearson, W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods. Enzymol. 183, 63-98.