title: Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors.
abstract: BACKGROUND
  Nucleotides are multifunctional molecules that are essential for numerous biological processes. They serve as sources for chemical energy, participate in the cellular signaling and they are involved in the enzymatic reactions. The knowledge of the nucleotide-protein interactions helps with annotation of protein functions and finds applications in drug design.
  
  
  RESULTS
  We propose a novel ensemble of accurate high-throughput predictors of binding residues from the protein sequence for ATP, ADP, AMP, GTP and GDP. Empirical tests show that our NsitePred method significantly outperforms existing predictors and approaches based on sequence alignment and residue conservation scoring. The NsitePred accurately finds more binding residues and binding sites and it performs particularly well for the sites with residues that are clustered close together in the sequence. The high predictive quality stems from the usage of novel, comprehensive and custom-designed inputs that utilize information extracted from the sequence, evolutionary profiles, several sequence-predicted structural descriptors and sequence alignment. Analysis of the predictive model reveals several sequence-derived hallmarks of nucleotide-binding residues; they are usually conserved and flanked by less conserved residues, and they are associated with certain arrangements of secondary structures and amino acid pairs in the specific neighboring positions in the sequence.
  
  
  BACKGROUND
  http://biomine.ece.ualberta.ca/nSITEpred/
  
  
  BACKGROUND
  lkurgan@ece.ualberta.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: School of Computer Science and Software Engineering, Tianjin Polytechnic University, Hedong District, Tianjin 300160, PR of China.
authors: Ke
authors: K
authors: Chen
authors: Marcin J
authors: MJ
authors: Mizianty
authors: Lukasz
authors: L
authors: Kurgan
mesh_terms: D001665:Binding Sites; D009711:Nucleotides / Q000737:chemistry / Q000378:metabolism*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D009711:Nucleotides; D011506:Proteins