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,^[1] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.

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:

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.

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]