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
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:
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
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)
References
- ^ "DSSP".
- S2CID 29185760.
- ^ a b "DSSP manual Archived 2015-05-22 at the Wayback Machine"
- PMID 20888342.
- PMID 11839303.