title: Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
abstract: BACKGROUND
  In the present work we combine computational analysis and experimental data to explore the extent to which binding site similarities between members of the human cytosolic sulfotransferase family correlate with small-molecule binding profiles. Conversely, from a small-molecule point of view, we explore the extent to which structural similarities between small molecules correlate to protein binding profiles.
  
  
  RESULTS
  The comparison of binding site structural similarities and small-molecule binding profiles shows that proteins with similar small-molecule binding profiles tend to have a higher degree of binding site similarity but the latter is not sufficient to predict small-molecule binding patterns, highlighting the difficulty of predicting small-molecule binding patterns from sequence or structure. Likewise, from a small-molecule perspective, small molecules with similar protein binding profiles tend to be topologically similar but topological similarity is not sufficient to predict their protein binding patterns. These observations have important consequences for function prediction and drug design.
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus Cambridge CB10 1SD, UK. rafael.najmanovich@ebi.ac.uk
authors.forename: Rafael J
authors.initials: RJ
authors.lastname: Najmanovich
authors.forename: Abdellah
authors.initials: A
authors.lastname: Allali-Hassani
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Morris
authors.forename: Ludmila
authors.initials: L
authors.lastname: Dombrovsky
authors.forename: Patricia W
authors.initials: PW
authors.lastname: Pan
authors.forename: Masoud
authors.initials: M
authors.lastname: Vedadi
authors.forename: Alexander N
authors.initials: AN
authors.lastname: Plotnikov
authors.forename: Aled
authors.initials: A
authors.lastname: Edwards
authors.forename: Cheryl
authors.initials: C
authors.lastname: Arrowsmith
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D006801:Humans; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D015238:Sulfotransferases / Q000737:chemistry*
chemical_list: D015238:Sulfotransferases