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STRIDE.
Last seen on: NY Times Crossword 11 May 22, Wednesday
Random information on the term “STRIDE”:
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, 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:
where the r A B {\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.