DSSP (algorithm)
| Original author(s) | Wolfgang Kabsch, Chris Sander |
|---|---|
| Developer(s) | Maarten Hekkelman[1] |
| Initial release | 1983 |
| Stable release | 4.4
/ 19 July 2023 |
| Repository | github |
| Written in | C++ |
| Operating system | Linux, Windows |
| License | BSD-2-clause license |
| Website | pdb-redo |
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.
Algorithm
[edit]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:
where the 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 and 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
[edit]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
[edit]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
[edit]- STRIDE (algorithm) an alternative algorithm
- Chris Sander (scientist)
References
[edit]- ^ "DSSP".
- ^ Kabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". Biopolymers. 22 (12): 2577–637. doi:10.1002/bip.360221211. PMID 6667333. S2CID 29185760.
- ^ a b "DSSP manual Archived 2015-05-22 at the Wayback Machine"
- ^ Cooley RB, Arp DJ, Karplus PA (2010). "Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices enhancing protein functionality". J Mol Biol. 404 (2): 232–246. doi:10.1016/j.jmb.2010.09.034. PMC 2981643. PMID 20888342.
- ^ Andersen CA, Palmer AG, Brunak S, Rost B (2002). "Continuum secondary structure captures protein flexibility". Structure. 10 (2): 175–184. doi:10.1016/S0969-2126(02)00700-1. PMID 11839303.