{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T00:21:59Z","timestamp":1772929319969,"version":"3.50.1"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivations: Characterizing protein\u2013protein interfaces and the hydrogen bonds is a first step to better understand proteins\u2019 structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody\u2013antigen interfaces is related to their evolutionary origin.<\/jats:p>\n               <jats:p>Results: Using 6637 non-redundant protein\u2013protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody\u2013antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity.<\/jats:p>\n               <jats:p>Contact: \u00a0jgray@jhu.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw197","type":"journal-article","created":{"date-parts":[[2016,4,20]],"date-time":"2016-04-20T01:30:19Z","timestamp":1461115819000},"page":"2451-2456","source":"Crossref","is-referenced-by-count":82,"title":["Shape complementarity and hydrogen bond preferences in protein\u2013protein interfaces: implications for antibody modeling and protein\u2013protein docking"],"prefix":"10.1093","volume":"32","author":[{"given":"Daisuke","family":"Kuroda","sequence":"first","affiliation":[{"name":"1 Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA,"},{"name":"2 Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, 142-8555, Japan"}]},{"given":"Jeffrey J.","family":"Gray","sequence":"additional","affiliation":[{"name":"1 Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA,"},{"name":"3 Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,4,19]]},"reference":[{"key":"2023020112515667700_btw197-B1","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1093\/protein\/gzq043","article-title":"Analysis and prediction of VH\/VL packing in antibodies","volume":"23","author":"Abhinandan","year":"2010","journal-title":"Protein Eng. 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