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Biol."],"published-print":{"date-parts":[[2018,6]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Protein\u2010protein interactions are essential to many biological processes. The binding site information of protein\u2010protein complexes is extremely useful to obtain their structures from biochemical experiments. Geometric description of protein structures is the precondition of protein binding site prediction and protein\u2010protein interaction analysis. The previous description of protein surface residues is incomplete, and little attention are paid to the implication of residue types for binding site prediction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Here, we found three new geometric features to characterize protein surface residues which are very effective for protein\u2010protein interface residue prediction. The new features and several commonly used descriptors were employed to train millions of residue type\u2010nonspecific or specific protein binding site predictors.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The amino acid type\u2010specific predictors are superior to the models without distinction of amino acid types. The performances of the best predictors are much better than those of the sophisticated methods developed before.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The results demonstrate that the geometric properties and amino acid types are very likely to determine if a protein surface residue would become an interface one when the protein binds to its partner.<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-018-0138-5","type":"journal-article","created":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T06:18:16Z","timestamp":1527056296000},"page":"163-174","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Geometric and amino acid type determinants for protein\u2010protein interaction interfaces"],"prefix":"10.1002","volume":"6","author":[{"given":"Yongxiao","family":"Yang","sequence":"first","affiliation":[{"name":"<!--1--> Institute for Mathematical Sciences Renmin University of China Beijing 100872 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"<!--2--> School of Statistics Renmin University of China Beijing 100872 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Lou","sequence":"additional","affiliation":[{"name":"<!--1--> Institute for Mathematical Sciences Renmin University of China Beijing 100872 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianxin","family":"Yin","sequence":"additional","affiliation":[{"name":"<!--2--> School of Statistics Renmin University of China Beijing 100872 China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinqi","family":"Gong","sequence":"additional","affiliation":[{"name":"<!--1--> Institute for Mathematical Sciences Renmin University of China Beijing 100872 China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2018,6]]},"reference":[{"key":"e_1_2_9_2_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1012820107"},{"key":"e_1_2_9_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/256705a0"},{"key":"e_1_2_9_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.1.13"},{"key":"e_1_2_9_5_2","doi-asserted-by":"publisher","DOI":"10.1021\/cr040409x"},{"key":"e_1_2_9_6_2","doi-asserted-by":"publisher","DOI":"10.1002\/anie.199423751"},{"key":"e_1_2_9_7_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.suppl_2.S249"},{"key":"e_1_2_9_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1005894107"},{"key":"e_1_2_9_9_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13015\u2010015\u20100033\u20109"},{"key":"e_1_2_9_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv027"},{"key":"e_1_2_9_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv009"},{"key":"e_1_2_9_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2015.10.003"},{"key":"e_1_2_9_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.7.980"},{"key":"e_1_2_9_14_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0087107"},{"key":"e_1_2_9_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm434"},{"key":"e_1_2_9_16_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201012\u2010352"},{"key":"e_1_2_9_17_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr311"},{"key":"e_1_2_9_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2016.08.014"},{"key":"e_1_2_9_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2015.07.016"},{"key":"e_1_2_9_20_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22830"},{"key":"e_1_2_9_21_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22106"},{"key":"e_1_2_9_22_2","unstructured":"Hubbard S.J.andThornton M.(1993)Naccess Version 2.1.1. 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