Nucleic Acids Research, 2003, Vol. 31, No. 13 3293-3295
© 2003 Oxford University Press
DSSPcont: continuous secondary structure assignments for proteins
1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA 2 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA 3 BASF AG, Carl-Bosch-Straße 38, 67056 Ludwigshafen, Germany 4 Structural Bioinformatics Group, Department of Biological Sciences, Imperial College, London, UK 5 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA
*To whom correspondence should be addressed. Tel: +1 2123053773; Fax: +1 2123057932; Email: carter{at}cubic.bioc.columbia.edu
The DSSP program automatically assigns the secondary structure for each residue from the three-dimensional co-ordinates of a protein structure to one of eight states. However, discrete assignments are incomplete in that they cannot capture the continuum of thermal fluctuations. Therefore, DSSPcont (http://cubic.bioc.columbia.edu/services/DSSPcont) introduces a continuous assignment of secondary structure that replaces ‘static’ by ‘dynamic’ states. Technically, the continuum results from calculating weighted averages over 10 discrete DSSP assignments with different hydrogen bond thresholds. A DSSPcont assignment for a particular residue is a percentage likelihood of eight secondary structure states, derived from a weighted average of the ten DSSP assignments. The continuous assignments have two important features: (i) they reflect the structural variations due to thermal fluctuations as detected by NMR spectroscopy; and (ii) they reproduce the structural variation between many NMR models from one single model. Therefore, functionally important variation can be extracted from a single X-ray structure using the continuous assignment procedure.
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