DSSP - Revision history

Christoph: /* The DSSP code */

2009-01-08T17:42:28Z

‎The DSSP code

Christoph: /* See also */

2007-06-24T02:05:02Z

‎See also

Christoph: /* References */

2007-06-24T01:56:55Z

‎References

Christoph at 01:47, 24 June 2007

2007-06-24T01:47:20Z

Christoph at 01:44, 24 June 2007

2007-06-24T01:44:18Z

New page

The '''DSSP''' program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment.<ref name="Kabsch1983">Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". ''Biopolymers, 22(12):2577-2637. PMID: 6667333.''</ref> DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB). DSSP is also the program that calculates DSSP entries from PDB entries.

The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure.

==Usage==
''Note: See [http://swift.cmbi.ru.nl/gv/dssp/descrip.html Description of the DSSP program] for details.''

dssp [-na] [-v] pdb_file [dssp_file]
dssp [-na] [-v] -- [dssp_file]
dssp [-h] [-?] [-V]

===Command line options===
;<code>-na</code>: Disables the calculation of accessible surface.
;<code>-c</code>: Classic (pre-July 1995) format.
;<code>-v</code>: Verbose.
;<code>--</code>: Read from standard input.
;<code>-h -?</code>: Prints a help message.
;<code>-l</code>: Prints the license information.
;<code>-V</code>: Prints version, as in first line of the output.

==See also==
*[http://www.cbs.dtu.dk/services/InterMap3D-1.0/ InterMap3D] — predicts interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences.
*[[wikipedia:Frenet-Serret formulas]] (and the curvature and torsion concepts in differential geometry called the kappa-tau framework)

==References==
<references/>
===Further reading===
*Soumpasis DM, Strahm MC (2000). "Efficient identification and analysis of substructures in proteins using the kappa-tau framework: left turns and helix c-cap motifs". ''J Biomol Struct Dyn, 17(6):965-979. PMID: 10949164''.

==External links==
*[http://swift.cmbi.ru.nl/gv/dssp/ The DSSP software and database]

[[Category:Bioinformatics]]

@@ Line 4: / Line 4: @@
 ==The DSSP code==
   H = alpha helix
-  B = residue in isolated beta-bridge
+  I = 5 helix (pi helix)
-  E = extended strand, participates in beta ladder
+ G = 3-helix (3/10 helix)
-  G = 3-helix (3/10 helix)
-  I = 5 helix (pi helix)
+  E = extended strand, participates in beta ladder
-  T = hydrogen bonded turn
+  B = residue in isolated beta-bridge
   S = bend
 A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong.

← Older revision		Revision as of 01:47, 24 June 2007
Line 2:		Line 2:

	The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure.		The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure.
		+
		+	==The DSSP code==
		+	H = alpha helix
		+	B = residue in isolated beta-bridge
		+	E = extended strand, participates in beta ladder
		+	G = 3-helix (3/10 helix)
		+	I = 5 helix (pi helix)
		+	T = hydrogen bonded turn
		+	S = bend
		+
		+	A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong.

	==Usage==		==Usage==

@@ Line 32: / Line 32: @@
 ==See also==
 *[http://www.cbs.dtu.dk/services/InterMap3D-1.0/ InterMap3D] &mdash; predicts interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein sequences.
-*[[wikipedia:Frenet-Serret formulas]] (and the curvature and torsion concepts in differential geometry called the kappa-tau framework)
+*[[wikipedia:Frenet-Serret formulas|Frenet-Serret formulas]] (and the curvature and torsion concepts in differential geometry called the kappa-tau framework)
 ==References==

@@ Line 37: / Line 37: @@
 <references/>
 ===Further reading===
 *Soumpasis DM, Strahm MC (2000). "Efficient identification and analysis of substructures in proteins using the kappa-tau framework: left turns and helix c-cap motifs". ''J Biomol Struct Dyn, 17(6):965-979. PMID: 10949164''.