DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W182-5. doi: 10.1093/nar/gkl189.

Abstract

DiANNA is a recent state-of-the-art artificial neural network and web server, which determines the cysteine oxidation state and disulfide connectivity of a protein, given only its amino acid sequence. Version 1.0 of DiANNA uses a feed-forward neural network to determine which cysteines are involved in a disulfide bond, and employs a novel architecture neural network to predict which half-cystines are covalently bound to which other half-cystines. In version 1.1 of DiANNA, described here, we extend functionality by applying a support vector machine with spectrum kernel for the cysteine classification problem-to determine whether a cysteine is reduced (free in sulfhydryl state), half-cystine (involved in a disulfide bond) or bound to a metallic ligand. In the latter case, DiANNA predicts the ligand among iron, zinc, cadmium and carbon. Available at: http://bioinformatics.bc.edu/clotelab/DiANNA/.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Artificial Intelligence*
  • Cysteine / chemistry*
  • Cysteine / classification*
  • Disulfides / chemistry
  • Internet
  • Oxidation-Reduction
  • Proteins / chemistry*
  • Sequence Analysis, Protein
  • Software*
  • User-Computer Interface

Substances

  • Disulfides
  • Proteins
  • Cysteine