title: ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model.
abstract: BACKGROUND
  The identification of protein-protein interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational tools for predicting PPI sites can fill the gaps of PPI present knowledge.
  
  
  RESULTS
  We present ISPRED4, an improved structure-based predictor of PPI sites on unbound monomer surfaces. ISPRED4 relies on machine-learning methods and it incorporates features extracted from protein sequence and structure. Cross-validation experiments are carried out on a new dataset that includes 151 high-resolution protein complexes and indicate that ISPRED4 achieves a per-residue Matthew Correlation Coefficient of 0.48 and an overall accuracy of 0.85. Benchmarking results show that ISPRED4 is one of the top-performing PPI site predictors developed so far.
  
  
  BACKGROUND
  gigi@biocomp.unibo.it.
  
  
  METHODS
  ISPRED4 and datasets used in this study are available at http://ispred4.biocomp.unibo.it .
authors.affiliation: Biocomputing Group, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.|CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.
authors.forename: Castrense
authors.initials: C
authors.lastname: Savojardo
authors.affiliation: Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Padova, Italy.
authors.forename: Piero
authors.initials: P
authors.lastname: Fariselli
authors.affiliation: Biocomputing Group, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.|CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Martelli
authors.affiliation: Biocomputing Group, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.|CIG, Interdepartmental Center «Luigi Galvani» for Integrated Studies of Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy.
authors.forename: Rita
authors.initials: R
authors.lastname: Casadio
mesh_terms: D019295:Computational Biology / Q000379:methods*; D000069550:Machine Learning; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software