{"id":914,"date":"2017-01-10T17:55:20","date_gmt":"2017-01-10T08:55:20","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=914"},"modified":"2017-01-12T10:37:37","modified_gmt":"2017-01-12T01:37:37","slug":"%e5%ae%9a%e9%87%8f%e7%9a%84%e9%85%8d%e5%88%97%e6%b4%bb%e6%80%a7%e3%83%a2%e3%83%87%e3%83%ab%ef%bc%8cpls%e5%9b%9e%e5%b8%b0","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2017\/01\/10\/%e5%ae%9a%e9%87%8f%e7%9a%84%e9%85%8d%e5%88%97%e6%b4%bb%e6%80%a7%e3%83%a2%e3%83%87%e3%83%ab%ef%bc%8cpls%e5%9b%9e%e5%b8%b0\/","title":{"rendered":"\u5b9a\u91cf\u7684\u914d\u5217\u6d3b\u6027\u30e2\u30c7\u30eb\uff0cPLS\u56de\u5e30"},"content":{"rendered":"<p>\u76ee\u7684: \u53d7\u5bb9\u4f53\u306e\u4e00\u6b21\u69cb\u9020\u304b\u3089\u30ea\u30ac\u30f3\u30c9\u89aa\u548c\u6027\u3092\u4e88\u6e2c\u3059\u308b\u30e2\u30c7\u30eb\u3092\u4f5c\u308b\uff0e<br \/>\n\u74b0\u5883: R 3.3.2 GUI 1.68 Mavericks build (7288).<br \/>\n\u53c2\u8003\u30b5\u30a4\u30c8: <a href=\"https:\/\/www.r-bloggers.com\/r-predicting-a-test-set-gasoline\/\">&#8220;R&#8221;: Predicting a Test Set (Gasoline)<\/a><\/p>\n<p>\u30b1\u30e2\u30e1\u30c8\u30ea\u30af\u30b9\uff08\u5316\u5b66\u8a08\u91cf\u5b66\uff09\u306e\u624b\u6cd5\u306b\u3064\u3044\u3066\u5b9f\u7fd2\u3057\u305f\u306e\u3067\u30e1\u30e2\uff0e<\/p>\n<p>\u5b9a\u91cf\u7684\u914d\u5217\u6d3b\u6027\u30e2\u30c7\u30eb\uff08Quantitative sequence-activity model\uff0cQSAM\uff09\u306f\uff0c\u6bd4\u8f03\u7684\u77ed\u3044DNA\uff0cRNA\uff0c\u30da\u30d7\u30c1\u30c9\u306e\u5b9a\u91cf\u7684\u69cb\u9020\u6d3b\u6027\u76f8\u95a2\uff08QSAR\uff09\u3067\u4f7f\u7528\u3055\u308c\u308b\u624b\u6cd5\u3067\u3059\u304c\uff0c\u4eca\u56de\u306f\u4e2d\u7a0b\u5ea6\u306e\u30bf\u30f3\u30d1\u30af\u8cea\u30c9\u30e1\u30a4\u30f3\u306b\u5bfe\u3057\u3066\u9069\u7528\u3057\u3066\u307f\u308b\u3053\u3068\u306b\u3057\u307e\u3057\u305f\uff0e<\/p>\n<h2>\u7d71\u8a08\u30bd\u30d5\u30c8R\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n<pre class=\"command-line\"><code class=\"language-bash\" data-line=\"\">$ brew tap caskroom\/cask\n$ brew cask install r-app<\/code><\/pre>\n<p>GUI\u7248\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3057\u305f\uff0e<\/p>\n<h2>\u30c8\u30ec\u30fc\u30cb\u30f3\u30b0\u30bb\u30c3\u30c8<\/h2>\n<p>C1\u30c9\u30e1\u30a4\u30f3\u306e\u4e00\u6b21\u69cb\u9020\uff08\u30a2\u30df\u30ce\u9178\u914d\u5217\uff0cPKC\u306f\u30e9\u30c3\u30c8\u306e\u914d\u5217\uff09\u3068\u30ea\u30ac\u30f3\u30c9 ([<sup>3<\/sup>H]phorbol-12,13-dibutyrate) \u306e\u89e3\u96e2\u5b9a\u6570<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>.<\/p>\n<p>Irie(1999), Shindo(2003), Irie(2004) \u304b\u3089\u89e3\u96e2\u5b9a\u6570<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u306e\u30c7\u30fc\u30bf\u3092\u62bd\u51fa\u3057\u307e\u3057\u305f\uff0e<\/p>\n<pre class=\"prettyprint\">PKCa-C1A              HKFIARFFKQPTFCSHCTDFIWG-FGKQGFQCQVCCFVVHKRCHEFVTFSC\r\nPKCb-C1A              HKFTARFFKQPTFCSHCTDFIWG-FGKQGFQCQVCCFVVHKRCHEFVTFSC\r\nPKCg-C1A              HKFTARFFKQPTFCSHCTDFIWG-IGKQGLQCQVCSFVVHRRCHEFVTFEC\r\nPKCd-C1A              HEFIATFFGQPTFCSVCKEFVWG-LNKQGYKCRQCNAAIHKKCIDKIIGRC\r\nPKCe-C1A              HKFMATYLRQPTYCSHCRDFIWGVIGKQGYQCQVCTCVVHKRCHELIITKC\r\nPKCh-C1A              HKFMATYLRQPTYCSHCREFIWGVFGKQGYQCQVCTCVVHKRCHHLIVTAC\r\nPKCq-C1A              HEFTATFFPQPTFCSVCHEFVWG-LNKQGYQCRRCNAAIHKKCIDKVIAKC\r\nPKCa-C1B              HKFKIHTYGSPTFCDHCGSLLYG-LIHQGMKCDTCDMNVHKQCVINVPSLC\r\nPKCb-C1B              HKFKIHTYSSPTFCDHCGSLLYG-LIHQGMKCDTCMMNVHKRCVMNVPSLC\r\nPKCg-C1B              HKFRLHSYSSPTFCDHCGSLLYG-LVHQGMKCSCCEMNVHRRCVRSVPSLC\r\nPKCd-C1B              HRFKVYNYMSPTFCDHCGTLLWG-LVKQGLKCEDCGMNVHHKCREKVANLC\r\nPKCe-C1B              HKFGIHNYKVPTFCDHCGSLLWG-LLRQGLQCKVCKMNVHRRCETNVAPNC\r\nPKCh-C1B              HKFNVHNYKVPTFCDHCGSLLWG-IMRQGLQCKICKMNVHIRCQANVAPNC\r\nPKCq-C1B              HRFKVYNYKSPTFCEHCGTLLWG-LARQGLKCDACGMNVHHRCQTKVANLC\r\nRasGRP1               HNFQETTYLKPTFCDNCAGFLWG-VIKQGYRCKDCGMNCHKQCKDLVVFEC\r\nRasGRP2               HNFQESNSLRPVACRHCKALILG-IYKQGLKCRACGVNCHKQCKDRLSVEC\r\nRasGRP3               HNFQEMTYLKPTFCEHCAGFLWG-IIKQGYKCKDCGANCHKQCKDLLVLAC\r\nRasGRP4               HTFHEVTFRKPTFCDSCSGFLWG-VTKQGYRCRECGLCCHKHCRDQVKVEC\r\na-chimaerin           HNFKVHTFRGPHWCEYCANFMWG-LIAQGVKCADCGLNVHKQCSKMVPNDC\r\nb-chimaerin           HNFKVHTFRGPHWCEYCANFMWG-LIAQGVRCSDCGLNVHKQCSKHVPNDC\r\nUnc13(C.elegans)      HNFATTTFQTPTFCYECEGLLWG-LARQGLRCTQCQVKVHDKCRELLSADC\r\nMunc13(human)         HNFEVWTATTPTYCYECEGLLWG-IARQGMRCTECGVKCHEKCQDLLNADC\r\nPKD-C1A               HALFVHSYRAPAFCDHCGEMLWG-LVRQGLKCEGCGLNYHKRCAFKIPNNC\r\nPKD-C1B               HTFVIHSYTRPTVCQYCKKLLKG-LFRQGLQCKDCRFNCHKRCAPKVPNNC\r\nDGKb-C1A(rat)         HVWRLKHFNKPAYCNLCLNMLIG-VGKQGLCCSFCKYTVHERCA-RAPPSC\r\nDGKb-C1A(human)       HVWRLKHFNKPAYCNLCLNMLIG-VGKQGLCCSFCKYTVHERCVARAPPSC\r\nDGKg-C1A              HAWTMKHFKKPTYCNFCHIMLMG-VRKQGLCCTYCKYTVHERCVSRNIPGC\r\n                      *         *  *  *  :: * .  **  *  *    * :*       *\r\n<\/pre>\n<p>\u30a2\u30df\u30ce\u9178\u914d\u5217\u306f\u305d\u306e\u307e\u307e\u3067\u306f\u5b9a\u91cf\u7684\u306b\u6271\u3046\u3053\u3068\u306f\u3067\u304d\u306a\u3044\u306e\u3067\uff0c\u4f55\u3089\u304b\u306e\u6570\u5024\uff08\u8a18\u8ff0\u5b50, descriptor\uff09\u3067\u30a2\u30df\u30ce\u9178\u6b8b\u57fa\u3092\u8868\u308f\u3059\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\uff0e\u3053\u308c\u307e\u3067\u306b\u69d8\u3005\u306a\u30a2\u30df\u30ce\u9178\u8a18\u8ff0\u5b50\u304c\u8003\u6848\u3055\u308c\u3066\u3044\u307e\u3059\u304c (Qian, 2017)\uff0c\u4eca\u56de\u306f\uff0cCollantes and Dunn III(1995) \u306b\u3088\u308b\u30a2\u30df\u30ce\u9178\u8a18\u8ff0\u5b50\uff0c\u3059\u306a\u308f\u3061\u7b49\u65b9\u6027\u8868\u9762\u7a4d\uff08isotropic surface area, <span style=\"font-style: bold;\">ISA<\/span>\uff09\u3068\u96fb\u8377\u6307\u6570\uff08electronic charge index, <span style=\"font-style: bold;\">ESI<\/span>\uff09\u3092\u4f7f\u7528\u3057\u307e\u3057\u305f\uff0eISA\u3068ESI\u306f\u3069\u3061\u3089\u3082\u6b63\u306e\u5024\u3067\uff0c\u305d\u308c\u305e\u308c\u30a2\u30df\u30ce\u9178\u5074\u9396\u306e\u5d69\u9ad8\u3055\u3068\u5c40\u6240\u7684\u306a\u6975\u6027\u3092\u8868\u308f\u3057\u3066\u3044\u307e\u3059\uff0e\u4f8b\u3048\u3070\uff0c\u30b0\u30ea\u30b7\u30f3\u306fISA = 19.93, ECI = 0.02\uff0c\u30d5\u30a7\u30cb\u30eb\u30a2\u30e9\u30cb\u30f3\u306fISA = 189.42, ECI = 0.14\uff0c\u30a2\u30eb\u30ae\u30cb\u30f3\u306fISA = 52.98\uff0cECI = 1.69\u3068\u306a\u3063\u3066\u3044\u307e\u3059\uff0e<\/p>\n<p>\u307e\u305a\uff0cExcel\u3067\u8868\u3092\u4f5c\u308aCSV\u5f62\u5f0f\u3067\u66f8\u304d\u51fa\u3057\u307e\u3059\uff0e\u30de\u30af\u30ed\u3092\u4e00\u56de\u66f8\u304f\u3068\u4ee5\u5f8c\u52b9\u7387\u7684\u3067\u3059\uff0ep<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub> = \u2212log <span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u3067\u3059\uff0e\u4ee5\u4e0b\u306e\u30d5\u30a1\u30a4\u30eb\u3092c1.csv\u3068\u3057\u3066\u4fdd\u5b58\u3057\u307e\u3059\uff0e\u30a2\u30e9\u30a4\u30f3\u30e1\u30f3\u30c8\u3057\u305f\u6642\u306e\u30ae\u30e3\u30c3\u30d7\u306b\u306fISA\uff0cECI\u5171\u306b\u50240\u3092\u5165\u308c\u307e\u3057\u305f\uff0e<\/p>\n<pre class=\"prettyprint\">peptide,pKd,ISA1,ISA2,ISA3,ISA4,ISA5,ISA6,ISA7,ISA8,ISA9,ISA10,ISA11,ISA12,ISA13,ISA14,ISA15,ISA16,ISA17,ISA18,ISA19,ISA20,ISA21,ISA22,ISA23,ISA24,ISA25,ISA26,ISA27,ISA28,ISA29,ISA30,ISA31,ISA32,ISA33,ISA34,ISA35,ISA36,ISA37,ISA38,ISA39,ISA40,ISA41,ISA42,ISA43,ISA44,ISA45,ISA46,ISA47,ISA48,ISA49,ISA50,ISA51,ECI1,ECI2,ECI3,ECI4,ECI5,ECI6,ECI7,ECI8,ECI9,ECI10,ECI11,ECI12,ECI13,ECI14,ECI15,ECI16,ECI17,ECI18,ECI19,ECI20,ECI21,ECI22,ECI23,ECI24,ECI25,ECI26,ECI27,ECI28,ECI29,ECI30,ECI31,ECI32,ECI33,ECI34,ECI35,ECI36,ECI37,ECI38,ECI39,ECI40,ECI41,ECI42,ECI43,ECI44,ECI45,ECI46,ECI47,ECI48,ECI49,ECI50,ECI51\r\na-C1A,8.96,87.38,102.8,189.4,149.8,62.9,52.98,189.4,189.4,102.8,19.53,122.4,59.44,189.4,78.51,19.75,87.38,78.51,59.44,18.46,189.4,149.8,179.2,19.93,0,189.4,19.93,102.8,19.53,19.93,189.4,19.53,78.51,19.53,120.9,78.51,78.51,189.4,120.9,120.9,87.38,102.8,52.98,78.51,87.38,30.19,189.4,120.9,59.44,189.4,19.75,78.51,0.56,0.53,0.14,0.09,0.05,1.69,0.14,0.14,0.53,1.36,0.16,0.65,0.14,0.15,0.56,0.56,0.15,0.65,1.25,0.14,0.09,1.08,0.02,0,0.14,0.02,0.53,1.36,0.02,0.14,1.36,0.15,1.36,0.07,0.15,0.15,0.14,0.07,0.07,0.56,0.53,1.69,0.15,0.56,1.31,0.14,0.07,0.65,0.14,0.56,0.15\r\nb-C1A,8.89,87.38,102.8,189.4,59.44,62.9,52.98,189.4,189.4,102.8,19.53,122.4,59.44,189.4,78.51,19.75,87.38,78.51,59.44,18.46,189.4,149.8,179.2,19.93,0,189.4,19.93,102.8,19.53,19.93,189.4,19.53,78.51,19.53,120.9,78.51,78.51,189.4,120.9,120.9,87.38,102.8,52.98,78.51,87.38,30.19,189.4,120.9,59.44,189.4,19.75,78.51,0.56,0.53,0.14,0.65,0.05,1.69,0.14,0.14,0.53,1.36,0.16,0.65,0.14,0.15,0.56,0.56,0.15,0.65,1.25,0.14,0.09,1.08,0.02,0,0.14,0.02,0.53,1.36,0.02,0.14,1.36,0.15,1.36,0.07,0.15,0.15,0.14,0.07,0.07,0.56,0.53,1.69,0.15,0.56,1.31,0.14,0.07,0.65,0.14,0.56,0.15\r\ng-C1A,8.82,87.38,102.8,189.4,59.44,62.9,52.98,189.4,189.4,102.8,19.53,122.4,59.44,189.4,78.51,19.75,87.38,78.51,59.44,18.46,189.4,149.8,179.2,19.93,0,149.8,19.93,102.8,19.53,19.93,154.4,19.53,78.51,19.53,120.9,78.51,19.75,189.4,120.9,120.9,87.38,52.98,52.98,78.51,87.38,30.19,189.4,120.9,59.44,189.4,30.19,78.51,0.56,0.53,0.14,0.65,0.05,1.69,0.14,0.14,0.53,1.36,0.16,0.65,0.14,0.15,0.56,0.56,0.15,0.65,1.25,0.14,0.09,1.08,0.02,0,0.09,0.02,0.53,1.36,0.02,0.1,1.36,0.15,1.36,0.07,0.15,0.56,0.14,0.07,0.07,0.56,1.69,1.69,0.15,0.56,1.31,0.14,0.07,0.65,0.14,1.31,0.15\r\nd-C1A,7.28,87.38,30.19,189.4,59.44,62.9,59.44,189.4,189.4,19.93,19.53,122.4,59.44,189.4,78.51,19.75,120.9,78.51,102.8,30.19,189.4,120.9,179.2,19.93,0,154.4,17.87,102.8,19.53,19.93,132.2,102.8,78.51,52.98,19.53,78.51,17.87,62.9,62.9,149.8,87.38,102.8,102.8,78.51,149.8,18.46,102.8,149.8,149.8,19.93,52.98,78.51,0.56,1.31,0.14,0.65,0.05,0.65,0.14,0.14,0.02,1.36,0.16,0.65,0.14,0.15,0.56,0.07,0.15,0.53,1.31,0.14,0.07,1.08,0.02,0,0.1,1.31,0.53,1.36,0.02,0.72,0.53,0.15,1.69,1.36,0.15,1.31,0.05,0.05,0.09,0.56,0.53,0.53,0.15,0.09,1.25,0.53,0.09,0.09,0.02,1.69,0.15\r\ne-C1A,8.25,87.38,102.8,189.4,132.2,62.9,59.44,132.2,154.4,52.98,19.53,122.4,59.44,132.2,78.51,19.75,87.38,78.51,52.98,18.46,189.4,149.8,179.2,19.93,120.9,149.8,19.93,102.8,19.53,19.93,132.2,19.53,78.51,19.53,120.9,78.51,59.44,78.51,120.9,120.9,87.38,102.8,52.98,78.51,87.38,30.19,154.4,149.8,149.8,59.44,102.8,78.51,0.56,0.53,0.14,0.34,0.05,0.65,0.72,0.1,1.69,1.36,0.16,0.65,0.72,0.15,0.56,0.56,0.15,1.69,1.25,0.14,0.09,1.08,0.02,0.07,0.09,0.02,0.53,1.36,0.02,0.72,1.36,0.15,1.36,0.07,0.15,0.65,0.15,0.07,0.07,0.56,0.53,1.69,0.15,0.56,1.31,0.1,0.09,0.09,0.65,0.53,0.15\r\nh-C1A,8.37,87.38,102.8,189.4,132.2,62.9,59.44,132.2,154.4,52.98,19.53,122.4,59.44,132.2,78.51,19.75,87.38,78.51,52.98,30.19,189.4,149.8,179.2,19.93,120.9,189.4,19.93,102.8,19.53,19.93,132.2,19.53,78.51,19.53,120.9,78.51,59.44,78.51,120.9,120.9,87.38,102.8,52.98,78.51,87.38,87.38,154.4,149.8,120.9,59.44,62.9,78.51,0.56,0.53,0.14,0.34,0.05,0.65,0.72,0.1,1.69,1.36,0.16,0.65,0.72,0.15,0.56,0.56,0.15,1.69,1.31,0.14,0.09,1.08,0.02,0.07,0.14,0.02,0.53,1.36,0.02,0.72,1.36,0.15,1.36,0.07,0.15,0.65,0.15,0.07,0.07,0.56,0.53,1.69,0.15,0.56,0.56,0.1,0.09,0.07,0.65,0.05,0.15\r\nq-C1A,6.70,87.38,30.19,189.4,59.44,62.9,59.44,189.4,189.4,122.4,19.53,122.4,59.44,189.4,78.51,19.75,120.9,78.51,87.38,30.19,189.4,120.9,179.2,19.93,0,154.4,17.87,102.8,19.53,19.93,132.2,19.53,78.51,52.98,19.53,78.51,17.87,62.9,62.9,149.8,87.38,102.8,102.8,78.51,149.8,18.46,102.8,120.9,149.8,62.9,102.8,78.51,0.56,1.31,0.14,0.65,0.05,0.65,0.14,0.14,0.16,1.36,0.16,0.65,0.14,0.15,0.56,0.07,0.15,0.56,1.31,0.14,0.07,1.08,0.02,0,0.1,1.31,0.53,1.36,0.02,0.72,1.36,0.15,1.69,1.36,0.15,1.31,0.05,0.05,0.09,0.56,0.53,0.53,0.15,0.09,1.25,0.53,0.07,0.09,0.05,0.53,0.15\r\na-C1B,8.28,87.38,102.8,189.4,102.8,149.8,87.38,59.44,132.2,19.93,19.75,122.4,59.44,189.4,78.51,18.46,87.38,78.51,19.93,19.75,154.4,154.4,132.2,19.93,0,154.4,149.8,87.38,19.53,19.93,132.2,102.8,78.51,18.46,59.44,78.51,18.46,132.2,17.87,120.9,87.38,102.8,19.53,78.51,120.9,149.8,17.87,120.9,122.4,19.75,154.4,78.51,0.56,0.53,0.14,0.53,0.09,0.56,0.65,0.72,0.02,0.56,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.02,0.56,0.1,0.1,0.72,0.02,0,0.1,0.09,0.56,1.36,0.02,0.34,0.53,0.15,1.25,0.65,0.15,1.25,0.34,1.31,0.07,0.56,0.53,1.36,0.15,0.07,0.09,1.31,0.07,0.16,0.56,0.1,0.15\r\nb-C1B,8.89,87.38,102.8,189.4,102.8,149.8,87.38,59.44,132.2,19.75,19.75,122.4,59.44,189.4,78.51,18.46,87.38,78.51,19.93,19.75,154.4,154.4,132.2,19.93,0,154.4,149.8,87.38,19.53,19.93,132.2,102.8,78.51,18.46,59.44,78.51,132.2,132.2,17.87,120.9,87.38,102.8,52.98,78.51,120.9,132.2,17.87,120.9,122.4,19.75,154.4,78.51,0.56,0.53,0.14,0.53,0.09,0.56,0.65,0.72,0.56,0.56,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.02,0.56,0.1,0.1,0.72,0.02,0,0.1,0.09,0.56,1.36,0.02,0.34,0.53,0.15,1.25,0.65,0.15,0.34,0.34,1.31,0.07,0.56,0.53,1.69,0.15,0.07,0.34,1.31,0.07,0.16,0.56,0.1,0.15\r\ng-C1B,8.92,87.38,102.8,189.4,52.98,154.4,87.38,19.75,132.2,19.75,19.75,122.4,59.44,189.4,78.51,18.46,87.38,78.51,19.93,19.75,154.4,154.4,132.2,19.93,0,154.4,120.9,87.38,19.53,19.93,132.2,102.8,78.51,19.75,78.51,78.51,30.19,132.2,17.87,120.9,87.38,52.98,52.98,78.51,120.9,52.98,19.75,120.9,122.4,19.75,154.4,78.51,0.56,0.53,0.14,1.69,0.1,0.56,0.56,0.72,0.56,0.56,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.02,0.56,0.1,0.1,0.72,0.02,0,0.1,0.07,0.56,1.36,0.02,0.34,0.53,0.15,0.56,0.15,0.15,1.31,0.34,1.31,0.07,0.56,1.69,1.69,0.15,0.07,1.69,0.56,0.07,0.16,0.56,0.1,0.15\r\nd-C1B,9.28,87.38,52.98,189.4,102.8,120.9,132.2,17.87,132.2,132.2,19.75,122.4,59.44,189.4,78.51,18.46,87.38,78.51,19.93,19.75,154.4,154.4,179.2,19.93,0,154.4,120.9,102.8,19.53,19.93,154.4,102.8,78.51,30.19,18.46,78.51,19.93,132.2,17.87,120.9,87.38,87.38,102.8,78.51,52.98,30.19,102.8,120.9,62.9,17.87,154.4,78.51,0.56,1.69,0.14,0.53,0.07,0.72,1.31,0.72,0.34,0.56,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.02,0.56,0.1,0.1,1.08,0.02,0,0.1,0.07,0.53,1.36,0.02,0.1,0.53,0.15,1.31,1.25,0.15,0.02,0.34,1.31,0.07,0.56,0.56,0.53,0.15,1.69,1.31,0.53,0.07,0.05,1.31,0.1,0.15\r\ne-C1B,9.09,87.38,102.8,189.4,19.93,149.8,87.38,17.87,132.2,102.8,120.9,122.4,59.44,189.4,78.51,18.46,87.38,78.51,19.93,19.75,154.4,154.4,179.2,19.93,0,154.4,154.4,52.98,19.53,19.93,154.4,19.53,78.51,102.8,120.9,78.51,102.8,132.2,17.87,120.9,87.38,52.98,52.98,78.51,30.19,59.44,17.87,120.9,62.9,122.4,17.87,78.51,0.56,0.53,0.14,0.02,0.09,0.56,1.31,0.72,0.53,0.07,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.02,0.56,0.1,0.1,1.08,0.02,0,0.1,0.1,1.69,1.36,0.02,0.1,1.36,0.15,0.53,0.07,0.15,0.53,0.34,1.31,0.07,0.56,1.69,1.69,0.15,1.31,0.65,1.31,0.07,0.05,0.16,1.31,0.15\r\nh-C1B,9.35,87.38,102.8,189.4,17.87,120.9,87.38,17.87,132.2,102.8,120.9,122.4,59.44,189.4,78.51,18.46,87.38,78.51,19.93,19.75,154.4,154.4,179.2,19.93,0,149.8,132.2,52.98,19.53,19.93,154.4,19.53,78.51,102.8,149.8,78.51,102.8,132.2,17.87,120.9,87.38,149.8,52.98,78.51,19.53,62.9,17.87,120.9,62.9,122.4,17.87,78.51,0.56,0.53,0.14,1.31,0.07,0.56,1.31,0.72,0.53,0.07,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.02,0.56,0.1,0.1,1.08,0.02,0,0.09,0.34,1.69,1.36,0.02,0.1,1.36,0.15,0.53,0.09,0.15,0.53,0.34,1.31,0.07,0.56,0.09,1.69,0.15,1.36,0.05,1.31,0.07,0.05,0.16,1.31,0.15\r\nq-C1B,9.14,87.38,52.98,189.4,102.8,120.9,132.2,17.87,132.2,102.8,19.75,122.4,59.44,189.4,78.51,30.19,87.38,78.51,19.93,59.44,154.4,154.4,179.2,19.93,0,154.4,62.9,52.98,19.53,19.93,154.4,102.8,78.51,18.46,62.9,78.51,19.93,132.2,17.87,120.9,87.38,87.38,52.98,78.51,19.53,59.44,102.8,120.9,62.9,17.87,154.4,78.51,0.56,1.69,0.14,0.53,0.07,0.72,1.31,0.72,0.53,0.56,0.16,0.65,0.14,0.15,1.31,0.56,0.15,0.02,0.65,0.1,0.1,1.08,0.02,0,0.1,0.05,1.69,1.36,0.02,0.1,0.53,0.15,1.25,0.05,0.15,0.02,0.34,1.31,0.07,0.56,0.56,1.69,0.15,1.36,0.65,0.53,0.07,0.05,1.31,0.1,0.15\r\nRasGRP1,9.14,87.38,17.87,189.4,19.53,30.19,59.44,59.44,132.2,154.4,102.8,122.4,59.44,189.4,78.51,18.46,17.87,78.51,62.9,19.93,189.4,154.4,179.2,19.93,0,120.9,149.8,102.8,19.53,19.93,132.2,52.98,78.51,102.8,18.46,78.51,19.93,132.2,17.87,78.51,87.38,102.8,19.53,78.51,102.8,18.46,154.4,120.9,120.9,189.4,30.19,78.51,0.56,1.31,0.14,1.36,1.31,0.65,0.65,0.72,0.1,0.53,0.16,0.65,0.14,0.15,1.25,1.31,0.15,0.05,0.02,0.14,0.1,1.08,0.02,0,0.07,0.09,0.53,1.36,0.02,0.72,1.69,0.15,0.53,1.25,0.15,0.02,0.34,1.31,0.15,0.56,0.53,1.36,0.15,0.53,1.25,0.1,0.07,0.07,0.14,1.31,0.15\r\nRasGRP2,6.00,87.38,17.87,189.4,19.53,30.19,19.75,17.87,19.75,154.4,52.98,122.4,120.9,62.9,78.51,52.98,87.38,78.51,102.8,62.9,154.4,149.8,154.4,19.93,0,149.8,132.2,102.8,19.53,19.93,154.4,102.8,78.51,52.98,62.9,78.51,19.93,120.9,17.87,78.51,87.38,102.8,19.53,78.51,102.8,18.46,52.98,154.4,19.75,120.9,30.19,78.51,0.56,1.31,0.14,1.36,1.31,0.56,1.31,0.56,0.1,1.69,0.16,0.07,0.05,0.15,1.69,0.56,0.15,0.53,0.05,0.1,0.09,0.1,0.02,0,0.09,0.72,0.53,1.36,0.02,0.1,0.53,0.15,1.69,0.05,0.15,0.02,0.07,1.31,0.15,0.56,0.53,1.36,0.15,0.53,1.25,1.69,0.1,0.56,0.07,1.31,0.15\r\nRasGRP3,8.82,87.38,17.87,189.4,19.53,30.19,132.2,59.44,132.2,154.4,102.8,122.4,59.44,189.4,78.51,30.19,87.38,78.51,62.9,19.93,189.4,154.4,179.2,19.93,0,149.8,149.8,102.8,19.53,19.93,132.2,102.8,78.51,102.8,18.46,78.51,19.93,62.9,17.87,78.51,87.38,102.8,19.53,78.51,102.8,18.46,154.4,154.4,120.9,154.4,62.9,78.51,0.56,1.31,0.14,1.36,1.31,0.34,0.65,0.72,0.1,0.53,0.16,0.65,0.14,0.15,1.31,0.56,0.15,0.05,0.02,0.14,0.1,1.08,0.02,0,0.09,0.09,0.53,1.36,0.02,0.72,0.53,0.15,0.53,1.25,0.15,0.02,0.05,1.31,0.15,0.56,0.53,1.36,0.15,0.53,1.25,0.1,0.1,0.07,0.1,0.05,0.15\r\nRasGRP4,8.97,87.38,59.44,189.4,87.38,30.19,120.9,59.44,189.4,52.98,102.8,122.4,59.44,189.4,78.51,18.46,19.75,78.51,19.75,19.93,189.4,154.4,179.2,19.93,0,120.9,59.44,102.8,19.53,19.93,132.2,52.98,78.51,52.98,30.19,78.51,19.93,154.4,78.51,78.51,87.38,102.8,87.38,78.51,52.98,18.46,19.53,120.9,102.8,120.9,30.19,78.51,0.56,0.65,0.14,0.56,1.31,0.07,0.65,0.14,1.69,0.53,0.16,0.65,0.14,0.15,1.25,0.56,0.15,0.56,0.02,0.14,0.1,1.08,0.02,0,0.07,0.65,0.53,1.36,0.02,0.72,1.69,0.15,1.69,1.31,0.15,0.02,0.1,0.15,0.15,0.56,0.53,0.56,0.15,1.69,1.25,1.36,0.07,0.53,0.07,1.31,0.15\r\na-chimaerin,8.32,87.38,17.87,189.4,102.8,120.9,87.38,59.44,189.4,52.98,19.93,122.4,87.38,179.2,78.51,30.19,132.2,78.51,62.9,17.87,189.4,132.2,179.2,19.93,0,154.4,149.8,62.9,19.53,19.93,120.9,102.8,78.51,62.9,18.46,78.51,19.93,154.4,17.87,120.9,87.38,102.8,19.53,78.51,19.75,102.8,132.2,120.9,122.4,17.87,18.46,78.51,0.56,1.31,0.14,0.53,0.07,0.56,0.65,0.14,1.69,0.02,0.16,0.56,1.08,0.15,1.31,0.72,0.15,0.05,1.31,0.14,0.34,1.08,0.02,0,0.1,0.09,0.05,1.36,0.02,0.07,0.53,0.15,0.05,1.25,0.15,0.02,0.1,1.31,0.07,0.56,0.53,1.36,0.15,0.56,0.53,0.34,0.07,0.16,1.31,1.25,0.15\r\nb-chimaerin,8.35,87.38,17.87,189.4,102.8,120.9,87.38,59.44,189.4,52.98,19.93,122.4,87.38,179.2,78.51,30.19,132.2,78.51,62.9,17.87,189.4,132.2,179.2,19.93,0,154.4,149.8,62.9,19.53,19.93,120.9,52.98,78.51,19.75,18.46,78.51,19.93,154.4,17.87,120.9,87.38,102.8,19.53,78.51,19.75,102.8,87.38,120.9,122.4,17.87,18.46,78.51,0.56,1.31,0.14,0.53,0.07,0.56,0.65,0.14,1.69,0.02,0.16,0.56,1.08,0.15,1.31,0.72,0.15,0.05,1.31,0.14,0.34,1.08,0.02,0,0.1,0.09,0.05,1.36,0.02,0.07,1.69,0.15,0.56,1.25,0.15,0.02,0.1,1.31,0.07,0.56,0.53,1.36,0.15,0.56,0.53,0.56,0.07,0.16,1.31,1.25,0.15\r\nunc13,8.52,87.38,17.87,189.4,62.9,59.44,59.44,59.44,189.4,19.53,59.44,122.4,59.44,189.4,78.51,132.2,30.19,78.51,30.19,19.93,154.4,154.4,179.2,19.93,0,154.4,62.9,52.98,19.53,19.93,154.4,52.98,78.51,59.44,19.53,78.51,19.53,120.9,102.8,120.9,87.38,18.46,102.8,78.51,52.98,30.19,154.4,154.4,19.75,62.9,18.46,78.51,0.56,1.31,0.14,0.05,0.65,0.65,0.65,0.14,1.36,0.65,0.16,0.65,0.14,0.15,0.72,1.31,0.15,1.31,0.02,0.1,0.1,1.08,0.02,0,0.1,0.05,1.69,1.36,0.02,0.1,1.69,0.15,0.65,1.36,0.15,1.36,0.07,0.53,0.07,0.56,1.25,0.53,0.15,1.69,1.31,0.1,0.1,0.56,0.05,1.25,0.15\r\nMunc13-1,6.70,87.38,17.87,189.4,30.19,120.9,179.2,59.44,62.9,59.44,59.44,122.4,59.44,132.2,78.51,132.2,30.19,78.51,30.19,19.93,154.4,154.4,179.2,19.93,0,149.8,62.9,52.98,19.53,19.93,132.2,52.98,78.51,19.75,30.19,78.51,19.93,120.9,102.8,78.51,87.38,30.19,102.8,78.51,19.53,18.46,154.4,154.4,17.87,62.9,18.46,78.51,0.56,1.31,0.14,1.31,0.07,1.08,0.65,0.05,0.65,0.65,0.16,0.65,0.72,0.15,0.72,1.31,0.15,1.31,0.02,0.1,0.1,1.08,0.02,0,0.09,0.05,1.69,1.36,0.02,0.34,1.69,0.15,0.56,1.31,0.15,0.02,0.07,0.53,0.15,0.56,1.31,0.53,0.15,1.36,1.25,0.1,0.1,1.31,0.05,1.25,0.15\r\nPKD-C1A,8.60,87.38,62.9,154.4,189.4,120.9,87.38,19.75,132.2,52.98,62.9,122.4,62.9,189.4,78.51,18.46,87.38,78.51,19.93,30.19,132.2,154.4,179.2,19.93,0,154.4,120.9,52.98,19.53,19.93,154.4,102.8,78.51,30.19,19.93,78.51,19.93,154.4,17.87,132.2,87.38,102.8,52.98,78.51,62.9,189.4,102.8,149.8,122.4,17.87,17.87,78.51,0.56,0.05,0.1,0.14,0.07,0.56,0.56,0.72,1.69,0.05,0.16,0.05,0.14,0.15,1.25,0.56,0.15,0.02,1.31,0.34,0.1,1.08,0.02,0,0.1,0.07,1.69,1.36,0.02,0.1,0.53,0.15,1.31,0.02,0.15,0.02,0.1,1.31,0.72,0.56,0.53,1.69,0.15,0.05,0.14,0.53,0.09,0.16,1.31,1.31,0.15\r\nPKD-C1B,8.57,87.38,59.44,189.4,120.9,149.8,87.38,19.75,132.2,59.44,52.98,122.4,59.44,120.9,78.51,19.53,189.4,78.51,102.8,102.8,154.4,154.4,102.8,19.93,0,154.4,189.4,52.98,19.53,19.93,154.4,19.53,78.51,102.8,18.46,78.51,52.98,189.4,17.87,78.51,87.38,102.8,52.98,78.51,62.9,122.4,102.8,120.9,122.4,17.87,17.87,78.51,0.56,0.65,0.14,0.07,0.09,0.56,0.56,0.72,0.65,1.69,0.16,0.65,0.07,0.15,1.36,0.14,0.15,0.53,0.53,0.1,0.1,0.53,0.02,0,0.1,0.14,1.69,1.36,0.02,0.1,1.36,0.15,0.53,1.25,0.15,1.69,0.14,1.31,0.15,0.56,0.53,1.69,0.15,0.05,0.16,0.53,0.07,0.16,1.31,1.31,0.15\r\nrDGKb-C1A,6.71,87.38,120.9,179.2,52.98,154.4,102.8,87.38,189.4,17.87,102.8,122.4,62.9,132.2,78.51,17.87,154.4,78.51,154.4,17.87,132.2,154.4,149.8,19.93,0,120.9,19.93,102.8,19.53,19.93,154.4,78.51,78.51,19.75,189.4,78.51,102.8,132.2,59.44,120.9,87.38,30.19,52.98,78.51,0,62.9,52.98,62.9,122.4,122.4,19.75,78.51,0.56,0.07,1.08,1.69,0.1,0.53,0.56,0.14,1.31,0.53,0.16,0.05,0.72,0.15,1.31,0.1,0.15,0.1,1.31,0.34,0.1,0.09,0.02,0,0.07,0.02,0.53,1.36,0.02,0.1,0.15,0.15,0.56,0.14,0.15,0.53,0.72,0.65,0.07,0.56,1.31,1.69,0.15,0,0.05,1.69,0.05,0.16,0.16,0.56,0.15\r\nhDGKb-C1A,7.87,87.38,120.9,179.2,52.98,154.4,102.8,87.38,189.4,17.87,102.8,122.4,62.9,132.2,78.51,17.87,154.4,78.51,154.4,17.87,132.2,154.4,149.8,19.93,0,120.9,19.93,102.8,19.53,19.93,154.4,78.51,78.51,19.75,189.4,78.51,102.8,132.2,59.44,120.9,87.38,30.19,52.98,78.51,120.9,62.9,52.98,62.9,122.4,122.4,19.75,78.51,0.56,0.07,1.08,1.69,0.1,0.53,0.56,0.14,1.31,0.53,0.16,0.05,0.72,0.15,1.31,0.1,0.15,0.1,1.31,0.34,0.1,0.09,0.02,0,0.07,0.02,0.53,1.36,0.02,0.1,0.15,0.15,0.56,0.14,0.15,0.53,0.72,0.65,0.07,0.56,1.31,1.69,0.15,0.07,0.05,1.69,0.05,0.16,0.16,0.56,0.15\r\nDGKg-C1A,8.55,87.38,62.9,179.2,59.44,132.2,102.8,87.38,189.4,102.8,102.8,122.4,59.44,132.2,78.51,17.87,189.4,78.51,87.38,149.8,132.2,154.4,132.2,19.93,0,120.9,52.98,102.8,19.53,19.93,154.4,78.51,78.51,59.44,132.2,78.51,102.8,132.2,59.44,120.9,87.38,30.19,52.98,78.51,120.9,19.75,52.98,17.87,149.8,122.4,19.93,78.51,0.56,0.05,1.08,0.65,0.34,0.53,0.56,0.14,0.53,0.53,0.16,0.65,0.72,0.15,1.31,0.14,0.15,0.56,0.09,0.34,0.1,0.34,0.02,0,0.07,1.69,0.53,1.36,0.02,0.1,0.15,0.15,0.65,0.72,0.15,0.53,0.72,0.65,0.07,0.56,1.31,1.69,0.15,0.07,0.56,1.69,1.31,0.09,0.16,0.02,0.15\r\n<\/pre>\n<h2>\u30c7\u30fc\u30bf\u306ePLS\u56de\u5e30\u5206\u6790<\/h2>\n<p><a href=\"http:\/\/www.ibm.com\/support\/knowledgecenter\/ja\/SSLVMB_22.0.0\/com.ibm.spss.statistics.help\/spss\/base\/idh_idd_pls_variables.htm\">\u504f\u6700\u5c0f\u4e8c\u4e57\uff08PLS\uff09\u56de\u5e30\u5206\u6790<\/a>\u3092\u4f7f\u7528\u3057\u307e\u3059\uff0eR-GUI\u3092\u8d77\u52d5\u3057\uff0c\u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3092CSV\u30d5\u30a1\u30a4\u30eb\u304c\u3042\u308b\u5834\u6240\u306b\u79fb\u52d5\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">&#91;R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0&#93;\r\n&gt; install.packages(&#34;pls&#34;)\r\n&gt; library(pls)\r\n&gt; c1 &lt;- read.csv(&#34;c1.csv&#34;,row.names=1)<\/pre>\n<p>\u5206\u6563\u304c0\uff08\u3064\u307e\u308a\u4fdd\u5b58\u3055\u308c\u3066\u3044\u308b\u30a2\u30df\u30ce\u9178\u6b8b\u57fa\uff09\u306e\u5217\uff08column\uff09\u3092\u524a\u9664\u3057\u307e\u3059\uff08HIS1, PRO11, CYS14, CYS17, GLY23, GLN27, GLY28, CYS31, CYS34, HIS39, CYS42, CYS50; \u756a\u53f7\u306fPKC\u03b4-C1B\u306e\u756a\u53f7\uff09<a href=\"http:\/\/lambdalisue.hatenablog.com\/entry\/2013\/07\/18\/134507\">\uff08\u3072\u3068\u76ee\u3067\u308f\u304b\u308b\u884c\u5217\uff08Row \u30fb Column\uff09\u306e\u65b9\u5411\u306e\u899a\u3048\u65b9<\/a>\uff09\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; c1.train &lt;- c1&#91;,apply(c1,2,var) != 0&#93; <\/pre>\n<p>PLS\u56de\u5e30\u5206\u6790\u3092\u884c\u3044\u307e\u3059\uff0ep<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u304c\u76ee\u7684\u5909\u6570\u3067\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; c1.pls &lt;- plsr(pKd ~ ., 15, data=c1.train, scale=TRUE, validation=&#34;CV&#34;)<\/pre>\n<p>pKd ~ \u306e\u5f8c\u306e\u30c9\u30c3\u30c8\uff08.\uff09\u306f\u6b8b\u308a\u5168\u90e8\u3068\u3044\u3046\u610f\u5473\uff0encomp\u306fPLS\u306e\u6f5c\u5728\u5909\u6570\u306e\u6700\u5927\u306e\u6570\u3067\u3059\uff0escale=T\u306f\u30aa\u30fc\u30c8\u30b9\u30b1\u30fc\u30eb\u3067\uff0c\u51e6\u7406\u306e\u524d\u306b\u30c7\u30fc\u30bf\u3092\u5e73\u57470\uff0c\u5206\u65631\u306b\u5909\u63db\u3057\u307e\u3059\uff0eCV\u306f<a href=\"http:\/\/support.minitab.com\/ja-jp\/minitab\/17\/topic-library\/modeling-statistics\/regression-and-correlation\/partial-least-squares-regression\/cross-validation-in-pls-regression\/\">\u4ea4\u5dee\u691c\u8a3c<\/a>\uff08cross validation\uff09\u306e\u7565\u3067\u3059\uff0e\u7d50\u679c\u3092summary\u3067\u898b\u3066\u307f\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; summary(c1.pls)\r\nData: \tX dimension: 27 78 \r\n\tY dimension: 27 1\r\nFit method: kernelpls\r\nNumber of components considered: 15\r\n\r\nVALIDATION: RMSEP\r\nCross-validated using 10 random segments.\r\n       (Intercept)  1 comps  2 comps  3 comps  4 comps  5 comps  6 comps  7 comps  8 comps  9 comps  10 comps  11 comps  12 comps  13 comps  14 comps  15 comps\r\nCV          0.9157    1.185    1.262    1.301    1.168    1.128   1.0501    1.015   0.9908   0.9676    0.9911    1.0024    1.0124    1.0168    1.0115    1.0055\r\nadjCV       0.9157    1.133    1.198    1.233    1.109    1.071   0.9985    0.965   0.9415   0.9179    0.9397    0.9498    0.9587    0.9625    0.9573    0.9516\r\n\r\nTRAINING: % variance explained\r\n     1 comps  2 comps  3 comps  4 comps  5 comps  6 comps  7 comps  8 comps  9 comps  10 comps  11 comps  12 comps  13 comps  14 comps  15 comps\r\nX      9.171    19.37    28.38    38.39    49.80    55.93    60.77    66.33    69.19     72.99     76.14     78.82     81.81     84.68     87.79\r\npKd   71.941    86.81    90.92    92.93    94.27    95.62    96.82    97.66    98.68     99.02     99.40     99.73     99.86     99.89     99.91<\/pre>\n<p>RMSEP\u306f\u300c\u4e88\u6e2c\u306e\u5e73\u5747\u5e73\u65b9\u6839\u8aa4\u5dee\u300d\uff08root mean squared error of prediction\uff09\u306e\u7565\u3067\u3059\uff0e\u3053\u306e\u5024\u304c\u5c0f\u3055\u3044\u7a0b\uff0c\u4e88\u6e2c\u5024\u3068\u30e2\u30c7\u30eb\u3068\u306e\u4e56\u96e2\u304c\u5c0f\u3055\u3044\u3053\u3068\u3092\u8868\u308f\u3057\u3066\u3044\u307e\u3059\uff0e\u4eca\u56de\u306f9\u3064\u306e\u6f5c\u5728\u5909\u6570\u3092\u4f7f\u7528\u3057\u305f\u5834\u5408\u306b\u3046\u307e\u304f\u30e2\u30c7\u30eb\u304c\u69cb\u7bc9\u3067\u304d\u3066\u3044\u308b\u3088\u3046\u3067\u3059\uff0e<br \/>\n\u4f7f\u7528\u3057\u305f\u30c7\u30fc\u30bf\u30bb\u30c3\u30c8\u306e\u30e2\u30c7\u30eb\u306b\u3088\u308b\u4e88\u6e2c\u5024\u3068\u5b9f\u6e2c\u5024\u3092\u30d7\u30ed\u30c3\u30c8\u3057\u3066\u307f\u307e\u3059\uff08\u4e0b\u56f3\uff09\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; plot(c1.train&#91;,1&#93;, c1.pls$fitted.value&#91;,,9&#93;, xlab=&#34;measured pKd&#34;, ylab=&#34;predicted pKd&#34;)<\/pre>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/01\/predicted-300x300.png\" alt=\"\" width=\"300\" height=\"300\" class=\"aligncenter size-medium wp-image-923\" srcset=\"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/01\/predicted-300x300.png 300w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/01\/predicted-150x150.png 150w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/01\/predicted-270x270.png 270w, https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp\/wp-content\/uploads\/2017\/01\/predicted.png 700w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/p>\n<h2>\u30e2\u30c7\u30eb\u306b\u3088\u308b\u4e88\u6e2c<\/h2>\n<h3>MRCK<\/h3>\n<p>Serine\/threonine-protein kinase MRCK\u03b1\/\u03b2\/\u03b3\u306e3\u7a2e\u306e\u30a2\u30a4\u30bd\u30b6\u30a4\u30e0\u306b\u542b\u307e\u308c\u308bC1\u30c9\u30e1\u30a4\u30f3\u306e[<sup>3<\/sup>H]PDBu\u7d50\u5408\u80fd\u3092\u524d\u7bc0\u3067\u4f5c\u3063\u305f\u56de\u5e30\u30e2\u30c7\u30eb\u3067\u4e88\u6e2c\u3057\u3066\u307f\u307e\u3059\uff08MRCK\u306fmyotonic dystrophy kinase related Cdc42-binding kinase\u306e\u7565\uff09\uff0e\u305d\u308c\u305e\u308c\u306e\u914d\u5217\u306f\u4ee5\u4e0b\u306e\u901a\u308a\u3067\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">\r\nMRCKa HQFFVKSFTT PTKCHQCTSL MVGLIRQGCS CEVCGFSCHI TCVNKAPTTC\r\nMRCKb HQFSIKSFSS PTQCSHCTSL MVGLIRQGYA CEVCSFACHV SCKDGAPQVC\r\nMRCKg HTLRPRSFPS PTKCLRCTSL MLGLGRQGLG CDACGYFCHT TCAPQAPP-C<\/pre>\n<p>\u3053\u308c\u3089\u306e\u914d\u5217\u304b\u3089ISA\u3068ECI\u306e\u5024\u3092\u542b\u3080CSV\u30d5\u30a1\u30a4\u30eb\uff08mrck.csv\uff09\u3092\u4f5c\u308a\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">peptide,pKd,ISA1,ISA2,ISA3,ISA4,ISA5,ISA6,ISA7,ISA8,ISA9,ISA10,ISA11,ISA12,ISA13,ISA14,ISA15,ISA16,ISA17,ISA18,ISA19,ISA20,ISA21,ISA22,ISA23,ISA24,ISA25,ISA26,ISA27,ISA28,ISA29,ISA30,ISA31,ISA32,ISA33,ISA34,ISA35,ISA36,ISA37,ISA38,ISA39,ISA40,ISA41,ISA42,ISA43,ISA44,ISA45,ISA46,ISA47,ISA48,ISA49,ISA50,ISA51,ECI1,ECI2,ECI3,ECI4,ECI5,ECI6,ECI7,ECI8,ECI9,ECI10,ECI11,ECI12,ECI13,ECI14,ECI15,ECI16,ECI17,ECI18,ECI19,ECI20,ECI21,ECI22,ECI23,ECI24,ECI25,ECI26,ECI27,ECI28,ECI29,ECI30,ECI31,ECI32,ECI33,ECI34,ECI35,ECI36,ECI37,ECI38,ECI39,ECI40,ECI41,ECI42,ECI43,ECI44,ECI45,ECI46,ECI47,ECI48,ECI49,ECI50,ECI51\r\nMRCKa,0,87.38,19.53,189.4,189.4,120.9,102.8,19.75,189.4,59.44,59.44,122.4,59.44,102.8,78.51,87.38,19.53,78.51,59.44,19.75,154.4,132.2,120.9,19.93,0,154.4,149.8,52.98,19.53,19.93,78.51,19.75,78.51,30.19,120.9,78.51,19.93,189.4,19.75,78.51,87.38,149.8,59.44,78.51,120.9,17.87,102.8,62.9,122.4,59.44,59.44,78.51,0.56,1.36,0.14,0.14,0.07,0.53,0.56,0.14,0.65,0.65,0.16,0.65,0.53,0.15,0.56,1.36,0.15,0.65,0.56,0.1,0.34,0.07,0.02,0,0.1,0.09,1.69,1.36,0.02,0.15,0.56,0.15,1.31,0.07,0.15,0.02,0.14,0.56,0.15,0.56,0.09,0.65,0.15,0.07,1.31,0.53,0.05,0.16,0.65,0.65,0.15\r\nMRCKb,0,87.38,19.53,189.4,19.75,149.8,102.8,19.75,189.4,19.75,19.75,122.4,59.44,19.53,78.51,19.75,87.38,78.51,59.44,19.75,154.4,132.2,120.9,19.93,0,154.4,149.8,52.98,19.53,19.93,132.2,62.9,78.51,30.19,120.9,78.51,19.75,189.4,62.9,78.51,87.38,120.9,19.75,78.51,102.8,18.46,19.93,62.9,122.4,19.53,120.9,78.51,0.56,1.36,0.14,0.56,0.09,0.53,0.56,0.14,0.56,0.56,0.16,0.65,1.36,0.15,0.56,0.56,0.15,0.65,0.56,0.1,0.34,0.07,0.02,0,0.1,0.09,1.69,1.36,0.02,0.72,0.05,0.15,1.31,0.07,0.15,0.56,0.14,0.05,0.15,0.56,0.07,0.56,0.15,0.53,1.25,0.02,0.05,0.16,1.36,0.07,0.15\r\nMRCKg,0,87.38,59.44,154.4,52.98,122.4,52.98,19.75,189.4,122.4,19.75,122.4,59.44,102.8,78.51,154.4,52.98,78.51,59.44,19.75,154.4,132.2,154.4,19.93,0,154.4,19.93,52.98,19.53,19.93,154.4,19.93,78.51,18.46,62.9,78.51,19.93,132.2,189.4,78.51,87.38,59.44,59.44,78.51,62.9,122.4,19.53,62.9,122.4,0,122.4,78.51,0.56,0.65,0.1,1.69,0.16,1.69,0.56,0.14,0.16,0.56,0.16,0.65,0.53,0.15,0.1,1.69,0.15,0.65,0.56,0.1,0.34,0.1,0.02,0,0.1,0.02,1.69,1.36,0.02,0.1,0.02,0.15,1.25,0.05,0.15,0.02,0.72,0.14,0.15,0.56,0.65,0.65,0.15,0.05,0.16,1.36,0.05,0.16,0,0.16,0.15<\/pre>\n<p>R\u3067\u3053\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u8aad\u307f\u8fbc\u307f\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; mrck &lt;- read.csv(&#34;mrck.csv&#34;, row.names=1)<\/pre>\n<p>\u30e2\u30c7\u30eb\u4f5c\u6210\u6642\u306b\u524a\u9664\u3057\u305f\u884c\u3092\u3053\u3061\u3089\u3067\u3082\u524a\u9664\u3057\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; mrck &lt;- mrck&#91;,c(-2,-12,-15,-18,-24,-29,-30,-33,-36,-41,-44,-52,-53,-63,-66,-69,-75,-80,-81,-84,-87,-92,-95,-103)&#93;<\/pre>\n<p>\u30e2\u30c7\u30eb\u3067\u4e88\u6e2c\u3057\u307e\u3059\uff08\u6f5c\u5728\u5909\u6570\u306e\u6570\u306f9\uff09\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; predict(c1.pls, ncomp=9, newdata=mrck)\r\n, , 9 comps\r\n\r\n           pKd\r\nMRCKa 7.565233\r\nMRCKb 7.209988\r\nMRCKg 5.848274\r\n<\/pre>\n<p>MRCK\u03b1\/\u03b2\/\u03b3\u306e [<sup>3<\/sup>H]PDBu\u306b\u5bfe\u3059\u308b\u4e88\u6e2c<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u306f\u305d\u308c\u305e\u308c\uff0c27, 62, 1400 nM\u3067\u3057\u305f\uff0eMRCK\u03b1\/\u03b2\u306e\u5b9f\u6e2c<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u306f\u305d\u308c\u305e\u308c10.3, 17 nM\u3068\u5831\u544a\u3055\u308c\u3066\u3044\u307e\u3059\uff08PKC\u03b4-C1B\u306e<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u306e\u305d\u308c\u305e\u308c58\uff0c96\u500d\uff09\uff08Choi, 2008\uff09\uff0e\u4eca\u56de\u4f7f\u7528\u3057\u305f\u30c7\u30fc\u30bf\u4e2d\u306ePKC\u03b4-C1B\u306e<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u306f0.53 nM\u306a\u306e\u3067\uff0c\u4e88\u6e2c\u5024\u306f\u305d\u308c\u305e\u308c51\uff0c117\u500d\u3068\u306a\u308a\uff0c\u5b9f\u9a13\u5024\u3068\u50be\u5411\u304c\u3088\u304f\u4e00\u81f4\u3057\u307e\u3057\u305f\uff0eMRCK\u03b3\u306e\u4e88\u6e2c<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u5024\u306f\u03bcM\u30aa\u30fc\u30c0\u30fc\u306a\u306e\u3067\uff0cMRCK\u03b3\u306fphorbol ester\u306b\u5bfe\u3057\u3066insensitive\u3067\u3042\u308b\u3068\u4e88\u60f3\u3055\u308c\u307e\u3059\uff0e<\/p>\n<h3>PKC\u03b4\u5909\u7570\u4f53<\/h3>\n<p>\u5929\u7136\u306e\u914d\u5217\u306e\u307f\u304b\u3089\u5b66\u7fd2\u3057\u305f\u30e2\u30c7\u30eb\u3067\u4eba\u70ba\u7684\u306b\u5909\u7570\u3092\u5165\u308c\u305f\u30c9\u30e1\u30a4\u30f3\u306e\u89aa\u548c\u6027\u3092\u4e88\u6e2c\u3067\u304d\u308b\u306e\u304b\uff0ePu(2014) \u3067\u306f\uff0cPKC\u03b4-C1B\u30c9\u30e1\u30a4\u30f3\u306ewild-type, N7R, S10R, P11R, L20R\u306e<span style=\"font-style: italic;\">K<\/span><sub>d<\/sub>\u304c\u5831\u544a\u3055\u308c\u3066\u3044\u308b\uff08\u305d\u308c\u305e\u308c\uff0c0.23, 1.18, 0.32, 1.19, 8.0 nM\uff09\uff0e\u4eca\u56de\u306e\u30e2\u30c7\u30eb\u3067\u306fPRO11\u304c\u4fdd\u5b58\u3055\u308c\u3066\u3044\u306a\u3044\u914d\u5217\u306f\u4e88\u6e2c\u3067\u304d\u306a\u3044\u305f\u3081\uff0c\u305d\u308c\u4ee5\u5916\u306e3\u7a2e\u985e\u306b\u3064\u3044\u3066\u4e88\u6e2c\u3057\u305f\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; predict(c1.pls, ncomp=9, newdata=mrck)\r\n, , 9 comps\r\n\r\n                pKd\r\nd-C1B_N7R  9.337275 #8.57\uff08\u88dc\u6b63\u6e08\u5b9f\u6e2c\u5024\uff09\r\nd-C1B_S10R 9.233776 #9.13\r\nd-C1B_L20R 8.748742 #7.74<\/pre>\n<p>\u3042\u307e\u308a\u4e00\u81f4\u3057\u3066\u3044\u306a\u304b\u3063\u305f\uff0e\u3053\u308c\u3089\u306e\u5909\u7570\u4f53\u3092\u30c8\u30ec\u30fc\u30cb\u30f3\u30b0\u30bb\u30c3\u30c8\u306b\u5165\u308c\u3066\u5b66\u7fd2\u3055\u305b\u305f\u30e2\u30c7\u30eb\u3067\u4e88\u6e2c\u3059\u308b\u3068\uff0c<\/p>\n<pre class=\"prettyprint\">                pKd\r\nd-C1B_N7R  8.943013 #8.57\uff08\u88dc\u6b63\u6e08\u5b9f\u6e2c\u5024\uff09\r\nd-C1B_S10R 9.084596 #9.13\r\nd-C1B_L20R 7.602420 #7.74<\/pre>\n<p>\u3068\uff08\u5f53\u7136\u3067\u3059\u304c\uff09\u5148\u7a0b\u3088\u308a\u4e00\u81f4\u3057\u307e\u3057\u305f\uff0e\u30c8\u30ec\u30fc\u30cb\u30f3\u30b0\u30bb\u30c3\u30c8\u306b\u3069\u306e\u30c7\u30fc\u30bf\u3092\u4f7f\u3046\u304b\u3067\uff0c\u4e88\u6e2c\u7cbe\u5ea6\u306f\u5927\u304d\u304f\u5909\u308f\u308a\u307e\u3059\uff0e<\/p>\n<h3>Human\u3068Rat\u306e\u914d\u5217\u306e\u9055\u3044<\/h3>\n<p>PKC\u03b4-C1A\uff0c\u03b4-C1B\uff0c\u304a\u3088\u3073\u03b7-C1B\u306f\u30d2\u30c8\u3068\u30e9\u30c3\u30c8\u3067\u914d\u5217\u306b\u308f\u305a\u304b\u306b\u9055\u3044\u304c\u3042\u308a\u307e\u3059\uff0e<\/p>\n<pre class=\"prettyprint\">PKCd-C1A(rat)        HEFIATFFGQPTFCSVCKEFVWGLNKQGYKCRQCNAAIHKKCIDKIIGRC\r\nPKCd-C1A(human)      HEFIATFFGQPTFCSVCKDFVWGLNKQGYKCRQCNAAIHKKCIDKIIGRC\r\nPKCd-C1B(rat)        HRFKVYNYMSPTFCDHCGTLLWGLVKQGLKCEDCGMNVHHKCREKVANLC\r\nPKCd-C1B(human)      HRFKVHNYMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVHHKCREKVANLC\r\nPKCh-C1B(rat)        HKFNVHNYKVPTFCDHCGSLLWGIMRQGLQCKICKMNVHIRCQANVAPNC\r\nPKCh-C1B(human)      HKFSIHNYKVPTFCDHCGSLLWGIMRQGLQCKICKMNVHIRCQANVAPNC<\/pre>\n<p>\u3053\u306e\u9055\u3044\u304c\u30ea\u30ac\u30f3\u30c9\u89aa\u548c\u6027\u306b\u5f71\u97ff\u3059\u308b\u304b\u3069\u3046\u304b\u4e88\u6e2c\uff0e<\/p>\n<pre class=\"prettyprint\">&gt; round(predict(c1.pls,ncomp=9,newdata=human),2)\r\n, , 9 comps\r\n\r\n            pKd\r\nd-C1A_human 7.31\r\nd-C1B_human 9.22\r\nh-C1B_human 9.28\r\nd-C1A_rat   7.32\r\nd-C1B_rat   9.25\r\nh-C1B_rat   9.37<\/pre>\n<h2>References<\/h2>\n<ul>\n<li>Irie, K.; Nakahara, A.; Ohigashi, H.; Fukuda, H.; Wender, P. A.; Konishi, H.; Kikkawa, U. Synthesis and phorbol ester-binding studies of the individual cysteine-rich motifs of protein Kinase D. <span style=\"font-style : italic;\">Bioorg. Med. Chem. Lett<\/span>. <span style=\"font-weight : bold;\">1999<\/span>, <span style=\"font-style : italic;\">9<\/span>, 2487\u20132490. DOI: <a href=\"http:\/\/dx.doi.org\/10.1016\/S0960-894X(99)00413-8\">10.1016\/S0960-894X(99)00413-8<\/a>. [PMID]: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10498194\/\">10498194<\/a>.<\/li>\n<li>Shindo, M.; Irie, K.; Masuda, A.; Ohigashi, H.; Shirai, Y.; Miyasaka, K.; Saito, N. Synthesis and phorbol ester binding of the cysteine-rich domains of diacylglycerol kinase (DGK) isozymes. <span style=\"font-style : italic;\">J. Biol. Chem<\/span>. <span style=\"font-weight : bold;\">2003<\/span>, <span style=\"font-style : italic;\">278<\/span>, 18448\u201318454. DOI: <a href=\"http:\/\/dx.doi.org\/10.1074\/jbc.M300400200\">10.1074\/jbc.M300400200<\/a>. [PMID]: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/12621060\/\">12621060<\/a>.<\/li>\n<li>Irie, K.; Masuda, A.; Shindo, M.; Nakagawa, Y.; Ohigashi, H. Tumor promoter binding of the protein kinase C C1 homology domain peptides of RasGRPs, chimaerins, and Unc13s. <span style=\"font-style : italic;\">Bioorg. Med. Chem<\/span>. <span style=\"font-weight : bold;\">2004<\/span>, <span style=\"font-style : italic;\">12<\/span>, 4575\u20134583. DOI: <a href=\"http:\/\/dx.doi.org\/10.1016\/j.bmc.2004.07.008\">10.1016\/j.bmc.2004.07.008<\/a>. [PMID]: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/15358285\/\">15358285<\/a>.<\/li>\n<li>Qian, Y.; Liang, Y.; Liu, W.; Liang, G. Comprehensive comparison of twenty structural characterization scales applied as QSAM of antimicrobial dodecapeptides derived from Bac2A against <span style=\"font-style : italic;\">P. aeruginosa<\/span>. <span style=\"font-style : italic;\">J. Mol. Graph. Model<\/span>. <span style=\"font-weight : bold;\">2017<\/span>, <span style=\"font-style : italic;\">71<\/span>, 88\u201395. DOI: <a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmgm.2016.11.003\">10.1016\/j.jmgm.2016.11.003<\/a>. [PMID]: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/27863328\/\">27863328<\/a>.<\/li>\n<li>Collantes, E. R.; Dunn, W. J. 3rd. Amino acid side chain descriptors for quantitative structure-activity relationship studies of peptide analogues. <span style=\"font-style : italic;\">J. Med. Chem<\/span>. <span style=\"font-weight : bold;\">1995<\/span>, <span style=\"font-style : italic;\">38<\/span>, 2705\u20132713. DOI: <a href=\"http:\/\/dx.doi.org\/10.1021\/jm00014a022\">10.1021\/jm00014a022<\/a>. [PMID]: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/7629809\/\">7629809<\/a>.<\/li>\n<li>Choi, S. H.; Czifra, G.; Kedei, N.; Lewin, N. E.; Lazar, J.; Pu, Y.; Marquez, V. E.; Blumberg, P. M. Characterization of the interaction of phorbol esters with the C1 domain of MRCK (myotonic dystrophy kinase-related Cdc42 binding kinase) \u03b1\/\u03b2. <span style=\"font-style : italic;\">J. Biol. Chem<\/span>. <span style=\"font-weight : bold;\">2008<\/span>, <span style=\"font-style : italic;\">283<\/span>, 10543\u201310549. DOI: <a href=\"http:\/\/dx.doi.org\/10.1074\/jbc.M707463200\">10.1074\/jbc.M707463200<\/a>. [PMID]: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/18263588\/\">18263588<\/a>.<\/li>\n<li>Pu, Y.; Kang, J. H.; Sigano, D. M.; Peach, M. L.; Lewin, N. E.; Marquez, V. E.; Blumberg, P. M. Diacylglycerol lactones targeting the structural features that distinguish the atypical C1 domains of protein kinase C \u03b6 and \u03b9 from typical C1 domains. <span style=\"font-style : italic;\">J. Med. Chem<\/span>. <span style=\"font-weight : bold;\">2014<\/span>, <span style=\"font-style : italic;\">57<\/span>, 3835\u20133844. DOI: <a href=\"http:\/\/dx.doi.org\/10.1021\/jm500165n\">10.1021\/jm500165n<\/a>. 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