title: A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange.
abstract: BACKGROUND
  To clarify the relationship between structural elements and polypeptide chain mobility, a set of statistical analyses of structures is necessary. Because at present proteins with determined spatial structures are much less numerous than those with amino acid sequence known, it is important to be able to predict the extent of proton protection from hydrogen-deuterium (HD) exchange basing solely on the protein primary structure.
  
  
  RESULTS
  Here we present a novel web server aimed to predict the degree of amino acid residue protection against HD exchange solely from the primary structure of the protein chain under study. On the basis of the amino acid sequence, the presented server offers the following three possibilities (predictors) for user's choice. First, prediction of the number of contacts occurring in this protein, which is shown to be helpful in estimating the number of protons protected against HD exchange (sensitivity 0.71). Second, probability of H-bonding in this protein, which is useful for finding the number of unprotected protons (specificity 0.71). The last is the use of an artificial predictor. Also, we report on mass spectrometry analysis of HD exchange that has been first applied to free amino acids. Its results showed a good agreement with theoretical data (number of protons) for 10 globular proteins (correlation coefficient 0.73). We pioneered in compiling two datasets of experimental HD exchange data for 35 proteins.
  
  
  BACKGROUND
  The H-Protection server is available for users at http://bioinfo.protres.ru/ogp/
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
authors.forename: Mikhail Yu
authors.initials: MY
authors.lastname: Lobanov
authors.forename: Masha Yu
authors.initials: MY
authors.lastname: Suvorina
authors.forename: Nikita V
authors.initials: NV
authors.lastname: Dovidchenko
authors.forename: Igor V
authors.initials: IV
authors.lastname: Sokolovskiy
authors.forename: Alexey K
authors.initials: AK
authors.lastname: Surin
authors.forename: Oxana V
authors.initials: OV
authors.lastname: Galzitskaya
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D041961:Deuterium Exchange Measurement; D020407:Internet; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D011522:Protons; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D011522:Protons