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DSSPcont: Continuous secondary structure assignments for proteins.

Phil Carter·Claus A F Andersen·Burkhard Rost
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Abstract

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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AlgorithmsAmino Acid SequenceHydrogen BondingInternetModels, MolecularNuclear Magnetic Resonance, BiomolecularProtein Structure, SecondaryProteinsSoftwareUser-Computer InterfaceJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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BibTeXRIS

Phil Carter, Claus A F Andersen, Burkhard Rost. 2003-07-01. DSSPcont: Continuous secondary structure assignments for proteins.. https://doi.org/10.1093/nar%2Fgkg626

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