GitHub - josch/stride: The original implementation of the structure identification (STRIDE) algorithm to identify protein secondary structure elements

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The original implementation of the structure identification (STRIDE) algorithm to identify protein secondary structure elements

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Name		Name	Last commit message	Last commit date
Latest commit History 4 Commits
doc		doc
Makefile		Makefile
README		README
area.c		area.c
asngener.c		asngener.c
chk_atom.c		chk_atom.c
chk_res.c		chk_res.c
chkchain.c		chkchain.c
command.c		command.c
contact_map.c		contact_map.c
contact_order.c		contact_order.c
core		core
die.c		die.c
dssp.c		dssp.c
elem.c		elem.c
escape.c		escape.c
filename.c		filename.c
fillasn.c		fillasn.c
geometry.c		geometry.c
hbenergy.c		hbenergy.c
helix.c		helix.c
hydrbond.c		hydrbond.c
initchn.c		initchn.c
measure.c		measure.c
memory.c		memory.c
mergepat.c		mergepat.c
molscr.c		molscr.c
nsc.c		nsc.c
nsc.h		nsc.h
one2thr.c		one2thr.c
outseq.c		outseq.c
p_atom.c		p_atom.c
p_compnd.c		p_compnd.c
p_endmdl.c		p_endmdl.c
p_expdta.c		p_expdta.c
p_helix.c		p_helix.c
p_jrnl.c		p_jrnl.c
p_model.c		p_model.c
p_rem.c		p_rem.c
p_sheet.c		p_sheet.c
p_ssbond.c		p_ssbond.c
p_turn.c		p_turn.c
pdb1fmc.pdb		pdb1fmc.pdb
pdb1mjh.pdb		pdb1mjh.pdb
pdb1res.pdb		pdb1res.pdb
pdb2btm.pdb		pdb2btm.pdb
pdbasn.c		pdbasn.c
phipsi.c		phipsi.c
place_h.c		place_h.c
protot.h		protot.h
rdmap.c		rdmap.c
rdpdb.c		rdpdb.c
report.c		report.c
sheet.c		sheet.c
splitstr.c		splitstr.c
ssbond.c		ssbond.c
stred.c		stred.c
stride.c		stride.c
stride.h		stride.h
stride.pdf		stride.pdf
strutil.c		strutil.c
thr2one.c		thr2one.c
tolostr.c		tolostr.c
turn.c		turn.c

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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 (1994) submitted

 - 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