DSSPcont: Continuous secondary structure assignments for proteins.

TitleDSSPcont: Continuous secondary structure assignments for proteins.
Publication TypeJournal Article
Year of Publication2003
AuthorsCarter, P, Andersen, CAF, Rost, B
JournalNucleic Acids Res
Date Published2003 Jul 1
KeywordsAlgorithms, Amino Acid Sequence, Hydrogen Bonding, Internet, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Structure, Secondary, Proteins, Software, User-Computer Interface

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.

Alternate JournalNucleic Acids Res.
PubMed ID12824310
PubMed Central IDPMC169032
Grant List1-P50-GM62413-01 / GM / NIGMS NIH HHS / United States
R01-GM63029-01 / GM / NIGMS NIH HHS / United States