Difference between revisions of "Dssp"

From Bioinformatikpedia
(Details)
 
Line 28: Line 28:
 
beta-ladders.
 
beta-ladders.
 
Geometrical features are bends, chirality, SS bonds and solvent exposure.
 
Geometrical features are bends, chirality, SS bonds and solvent exposure.
With these features dssp assigns the secondary structure (8 different states).
+
With these features DSSP assigns the secondary structure (8 different states).

Latest revision as of 21:10, 2 June 2011

DSSP - Define Secondary Structure of Proteins

Basic Information

Author Kabsch W, Sander C.
Year 1983
Reference PubMed 6667333

DSSP performs a search for patterns in the resolved structure of a protein. Therefore it predicts H-Bonds by a cutoff in the energy bond. It searches for "n-turns" and bridges. "n-turns" are H-Bonds between the 0H of residue i and the NH of residue i+n (n = 3 or 4 or 5; 4 is the classical alpha-Helix), whereas bridges are H-Bonds not near each other in sequence (repeated bridges form beta-Sheets).

Details

DSSP knowns different features and depending on the predicted features of an amino acid is the secondary structure assigned.

First it searches for H-Bonds by a cutoff in the energy bond. With the H-Bonds it searches for turns and bridges. These turns and bridges are used for the search of alpha-helices and beta-ladders. Geometrical features are bends, chirality, SS bonds and solvent exposure. With these features DSSP assigns the secondary structure (8 different states).