{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T13:11:53Z","timestamp":1758892313656},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: 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\u2013deuterium (HD) exchange basing solely on the protein primary structure.<\/jats:p>\n               <jats:p>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\u2019s 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.<\/jats:p>\n               <jats:p>Availability: The H-Protection server is available for users at http:\/\/bioinfo.protres.ru\/ogp\/<\/jats:p>\n               <jats:p>Contact: \u00a0ogalzit@vega.protres.ru<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt168","type":"journal-article","created":{"date-parts":[[2013,4,26]],"date-time":"2013-04-26T01:21:15Z","timestamp":1366939275000},"page":"1375-1381","source":"Crossref","is-referenced-by-count":14,"title":["A novel web server predicts amino acid residue protection against hydrogen\u2013deuterium exchange"],"prefix":"10.1093","volume":"29","author":[{"given":"Mikhail Yu.","family":"Lobanov","sequence":"first","affiliation":[{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"}]},{"given":"Masha Yu.","family":"Suvorina","sequence":"additional","affiliation":[{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"}]},{"given":"Nikita V.","family":"Dovidchenko","sequence":"additional","affiliation":[{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"}]},{"given":"Igor V.","family":"Sokolovskiy","sequence":"additional","affiliation":[{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"}]},{"given":"Alexey K.","family":"Surin","sequence":"additional","affiliation":[{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"},{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"}]},{"given":"Oxana V.","family":"Galzitskaya","sequence":"additional","affiliation":[{"name":"1 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia and 2State Research Center for Applied Microbiology & Biotechnology, Obolensk, Serpukhov district, Moscow Region, 142279, Russia"}]}],"member":"286","published-online":{"date-parts":[[2013,4,24]]},"reference":[{"key":"2023062610153532100_btt168-B1","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1002\/pro.5560060709","article-title":"Absence of a stable intermediate on the folding pathway of protein A","volume":"6","author":"Bai","year":"1997","journal-title":"Protein Sci."},{"key":"2023062610153532100_btt168-B2","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/346488a0","article-title":"Detection and characterization of a folding intermediate in Barnase by NMR","volume":"346","author":"Bycroft","year":"1990","journal-title":"Nature"},{"key":"2023062610153532100_btt168-B3","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1038\/nsb0996-782","article-title":"Detection of rare partially folded molecules in equilibrium with the native conformation of RNaseH","volume":"3","author":"Chamberlain","year":"1996","journal-title":"Nat. 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