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How to Use Protein 1- D Structure Predicted by PROFphd

  • Protocol
The Proteomics Protocols Handbook

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

The abbreviations used in this chapter are as follows:

  • â„¢ 1-D structure: one-dimensional structure, i.e., any structural feature that describes single residues, such as protein sequence or string of secondary structure and solvent accessibil- ity assignments per residue.

  • â„¢ 3-D structure: three-dimensional coordinates of protein structure.

  • â„¢ EVA: server automatically evaluating structure prediction methods (1– 3).

  • â„¢ META-PP: Internet service allowing access to a variety of bioinformatics tools through a single interface (4).

  • â„¢ PDB: Protein Data Bank of experimentally determined 3-D structures of proteins (5).

  • â„¢ PHDhtm: profile-based neural network prediction of transmembrane helices (6– 8).

  • â„¢ PHDpsi: divergent profile (PSI-BLAST) based neural network prediction (9).

  • â„¢ PP (PredictProtein): Internet server for protein sequence analysis and protein structure prediction (7,10,11).

  • â„¢ PROFphd: advanced profile-based neural network prediction of secondary structure (PROFsec) and solvent accessibility (PROFacc) (11).

  • â„¢ SWISS-PROT: data base of protein sequences (12).

  • â„¢ Notations used:

  • â„¢ Secondary structure: H = helix; E = strand; L = other.

  • â„¢ Solvent accessibility: e = exposed (≥16% relative accessible surface); b = buried (<16%).

  • â„¢ Transmembrane helices: T = transmembrane; N = globular.

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  1. CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, Columbia University Center for Computational Biology and Bioinformatics, NorthEast Structural Genomics Consortium, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY

    Burkhard Rost

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  1. University of Hertfordshire, Hatfield, UK

    John M. Walker

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Rost, B. (2005). How to Use Protein 1- D Structure Predicted by PROFphd. In: Walker, J.M. (eds) The Proteomics Protocols Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1385/1-59259-890-0:875

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  • DOI: https://doi.org/10.1385/1-59259-890-0:875

  • Publisher Name: Humana Press

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