title: Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
abstract: BACKGROUND
  Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns. However, none of them takes into consideration the relevance of protein subcellular localization.
  
  
  RESULTS
  Here we develop DISLOCATE, a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain. We find that the inclusion of protein subcellular localization improves the performance of these predictive steps by 3 and 2 percentage points, respectively. When compared with previously developed methods for predicting disulfide bonds from sequence, DISLOCATE improves the overall performance by more than 10 percentage points.
  
  
  BACKGROUND
  The method and the dataset are available at the Web page http://www.biocomp.unibo.it/savojard/Dislocate.html. GRHCRF code is available at http://www.biocomp.unibo.it/savojard/biocrf.html.
  
  
  BACKGROUND
  piero.fariselli@unibo.it.
authors.affiliation: Biocomputing Group, University of Bologna, CIRI-Life Science and Health Technologies and Department of Biology, Via San Giacomo 9/2, Bologna, Italy.
authors.forename: Castrense
authors.initials: C
authors.lastname: Savojardo
authors.forename: Piero
authors.initials: P
authors.lastname: Fariselli
authors.forename: Monther
authors.initials: M
authors.lastname: Alhamdoosh
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Martelli
authors.forename: Andrea
authors.initials: A
authors.lastname: Pierleoni
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
mesh_terms: D001185:Artificial Intelligence; D003545:Cysteine / Q000737:chemistry*; D004220:Disulfides / Q000737:chemistry*; D056890:Eukaryota; D011506:Proteins / Q000032:analysis / Q000737:chemistry*
chemical_list: D004220:Disulfides; D011506:Proteins; D003545:Cysteine