DSSP (algorithm)

The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm,^[2] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.

DSSP

Original author(s)	Wolfgang Kabsch, Chris Sander
Developer(s)	Maarten Hekkelman[1]
Initial release	1983
Stable release	4.4 / 19 July 2023; 21 months ago (2023-07-19)
Repository	github.com/PDB-REDO/dssp
Written in	C++
Operating system	Linux, Windows
License	BSD-2-clause license
Website	pdb-redo.eu/dssp/

Algorithm

DSSP begins by identifying the intra-backbone hydrogen bonds of the protein using a purely electrostatic definition, assuming partial charges of −0.42 e and +0.20 e to the carbonyl oxygen and amide hydrogen respectively, their opposites assigned to the carbonyl carbon and amide nitrogen. A hydrogen bond is identified if E in the following equation is less than -0.5 kcal/mol:

${\displaystyle E=0.084\left\{{\frac {1}{r_{ON}}}+{\frac {1}{r_{CH}}}-{\frac {1}{r_{OH}}}-{\frac {1}{r_{CN}}}\right\}\cdot 332\,\mathrm {kcal/mol} }$

where the ${\displaystyle r_{AB}}$ terms indicate the distance between atoms A and B, taken from the carbon (C) and oxygen (O) atoms of the C=O group and the nitrogen (N) and hydrogen (H) atoms of the N-H group.

Based on this, nine types of secondary structure are assigned. The 3₁₀ helix, α helix and π helix have symbols G, H and I and are recognized by having a repetitive sequence of hydrogen bonds in which the residues are three, four, or five residues apart respectively. Two types of beta sheet structures exist; a beta bridge has symbol B while longer sets of hydrogen bonds and beta bulges have symbol E. T is used for turns, featuring hydrogen bonds typical of helices, S is used for regions of high curvature (where the angle between ${\displaystyle {\overrightarrow {C_{i}^{\alpha }C_{i+2}^{\alpha }}}}$ and ${\displaystyle {\overrightarrow {C_{i-2}^{\alpha }C_{i}^{\alpha }}}}$ is at least 70°). As of DSSP version 4, PPII helices are also detected based on a combination of backbone torsion angles and the absence of hydrogen bonds compatible with other types. PPII helices have symbol P. A blank (or space) is used if no other rule applies, referring to loops.^[3] These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (S, T, and C, where C sometimes is represented also as blank space).

π helices

In the original DSSP algorithm, residues were preferentially assigned to α helices, rather than π helices. In 2011, it was shown that DSSP failed to annotate many "cryptic" π helices, which are commonly flanked by α helices.^[4] In 2012, DSSP was rewritten so that the assignment of π helices was given preference over α helices, resulting in better detection of π helices.^[3] Versions of DSSP from 2.1.0 onwards therefore produce slightly different output from older versions.

Variants

In 2002, a continuous DSSP assignment was developed by introducing multiple hydrogen bond thresholds, where the new assignment was found to correlate with protein motion.^[5]

See also

• STRIDE (algorithm) an alternative algorithm
• Chris Sander (scientist)