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:

:$$

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 $r\_\{AB\}$ 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 $\backslash overrightarrow\{C\_i^\backslash alpha\; C\_\{i+2\}^\backslash alpha\}$ and $\backslash overrightarrow\{C\_\{i-2\}^\backslash alpha\; C\_i^\backslash alpha\}$ 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."[http://swift.cmbi.ru.nl/gv/dssp/ DSSP manual] {{Webarchive|url=https://web.archive.org/web/20150522130722/http://swift.cmbi.ru.nl/gv/dssp/ |date=2015-05-22 }}" 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).

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.{{cite journal |doi=10.1016/j.jmb.2010.09.034 |vauthors=Cooley RB, Arp DJ, Karplus PA |year=2010 |title=Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices enhancing protein functionality|journal=J Mol Biol |volume=404 |issue=2 |pages=232–246 |pmid=20888342 |pmc=2981643}} 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. Versions of DSSP from 2.1.0 onwards therefore produce slightly different output from older versions.

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.{{cite journal |vauthors=Andersen CA, Palmer AG, Brunak S, Rost B |title=Continuum secondary structure captures protein flexibility |journal=Structure |volume=10 |issue=2 |pages=175–184 |year=2002 |pmid=11839303 |doi=10.1016/S0969-2126(02)00700-1|doi-access=free }}

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

{{reflist}}

• [https://web.archive.org/web/20090712140715/http://botdb.abcc.ncifcrf.gov/proteinAnal/dsspUpload.jsp DSSP Analysis tool]
• [http://rostlab.org/owiki/index.php/DSSPcont Continuous DSSP tool]

{{Protein secondary structure}}

Category:Protein structure