{"id":126,"date":"2019-05-04T15:29:03","date_gmt":"2019-05-04T06:29:03","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=126"},"modified":"2022-02-22T14:23:34","modified_gmt":"2022-02-22T05:23:34","slug":"ligandscout_virtual_screening","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2019\/05\/04\/ligandscout_virtual_screening\/","title":{"rendered":"LigandScout\u3067\u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0"},"content":{"rendered":"\n

\u4eca\u56de\u306f\u3001LigandScout\u3092\u7528\u3044\u305f\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u306e\u69cb\u7bc9\u3068\u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u3092\u884c\u3063\u3066\u307f\u307e\u3059\u3002<\/p>\n\n\n\n

\u4f8b\u3068\u3057\u3066\u3001DUD-E<\/a>\u304b\u3089PARP1\u306e\u963b\u5bb3\u5264\u3068\u305d\u306e\u30c7\u30b3\u30a4\u3092\u53d6\u5f97\u3057\u3066\u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u3092\u5b9f\u65bd\u3057\u307e\u3059\u3002DUD-E\u306f\u3001\u30c9\u30c3\u30ad\u30f3\u30b0\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u30d9\u30f3\u30c1\u30de\u30fc\u30af\u3092\u884c\u3046\u305f\u3081\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3067\u3042\u308a\u3001102\u306e\u6a19\u7684\u30bf\u30f3\u30d1\u30af\u8cea\u306b\u5bfe\u3057\u306622,886\u306e\u6d3b\u6027\u5206\u5b50\u304c\u767b\u9332\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u3055\u3089\u306b1\u3064\u306e\u6d3b\u6027\u5206\u5b50\u3042\u305f\u308a50\u500b\u306e\u30c7\u30b3\u30a4\u5206\u5b50\u304c\u767b\u9332\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u307e\u305a\u306f\u3001\u3053\u3053<\/a>\u304b\u3089actives_final.sdf.gz\u3068decoys_final.sdf.gz\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u307e\u3059\u3002<\/p>\n\n\n\n\n\n\n\n

Step 1: PARP1\u3068\u963b\u5bb3\u5264\u306e\u8907\u5408\u4f53\u69cb\u9020\u306e\u53d6\u5f97<\/strong><\/p>\n\n\n\n

LigandScout\u3092\u8d77\u52d5\u3057\u3001PDB 4-letter code\u3067\u3042\u308b”3l3m”\u3092\u5165\u529b\u3057\u3066\u53f3\u5074\u306e\u30dc\u30bf\u30f3\u3092\u62bc\u3059\u3068PDB\u304b\u3089\u30c7\u30fc\u30bf\u3092\u53d6\u5f97\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

Step 2: \u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u306e\u69cb\u7bc9<\/strong><\/p>\n\n\n\n

\u963b\u5bb3\u5264\u306e\u5468\u8fba\u306b\u3042\u308b\u9ec4\u8272\u306e\u56db\u89d2\u3067\u56f2\u307e\u308c\u3066\u3044\u308b\u9818\u57df\u3092\u30af\u30ea\u30c3\u30af\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

Water(\u8d64\u56db\u89d2)\u3092\u9078\u629e\u3057delete\u30ad\u30fc\u3092\u62bc\u3059\u3053\u3068\u3067\u6c34\u5206\u5b50\u3092\u524a\u9664\u3057\u307e\u3059\u3002\u305d\u306e\u5f8c\u3001\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u3092\u69cb\u7bc9\u3059\u308b\u305f\u3081\u306bpharmacophore\u30a2\u30a4\u30b3\u30f3(\u9752\u56db\u89d2)\u3092\u62bc\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u306e\u69cb\u7bc9\u304c\u3067\u304d\u307e\u3057\u305f\u3002Copy to other perspectives\u306e\u771f\u3093\u4e2d\u306e\u30dc\u30bf\u30f3\u3092\u62bc\u3057\u3066\u3001screening perspective\u3092\u9078\u629e\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

Step 3: \u6d3b\u6027\u5206\u5b50\u3068\u30c7\u30b3\u30a4\u5206\u5b50\u306e\u914d\u5ea7\u751f\u6210<\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

Screening\u30dc\u30bf\u30f3(\u9752\u56db\u89d2)\u3092\u62bc\u3057Screening perspective\u306b\u79fb\u52d5\u3057\u307e\u3059\u3002\u305d\u306e\u5f8c\u3001\u53f3\u4e0a\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u30a2\u30a4\u30b3\u30f3(\u8d64\u56db\u89d2)\u3092\u62bc\u3057\u307e\u3059\u3002Create Screening Database window\u304c\u958b\u304d\u307e\u3059\u306e\u3067\u3001Input File\u3092DUD-E\u304b\u3089\u53d6\u5f97\u3057\u305factives_final.sdf\u3068\u3057\u3001Output File\u3092actives_final.ldb\u3068\u3057\u3066Next\u30dc\u30bf\u30f3\u3092\u62bc\u3057\u307e\u3059\u3002\u672c\u64cd\u4f5c\u306b\u3088\u308a\u914d\u5ea7\u751f\u6210\u3092\u884c\u3046\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002\u30c7\u30b3\u30a4\u5206\u5b50\u3082\u540c\u69d8\u306e\u64cd\u4f5c\u3092\u884c\u3044\u307e\u3059\u3002<\/p>\n\n\n\n

Step 4: \u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0<\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u9752\u56db\u89d2\u5185\u306e\u30a2\u30a4\u30b3\u30f3\u3092\u62bc\u3057\u3066\u3001Step 3\u3067\u4f5c\u6210\u3057\u305factives_final.ldb\u3068decoys_final.ldb\u3092\u5165\u529b\u3057\u307e\u3059\u3002actives_final.ldb\u306e\u5de6\u5074\u306e\u30de\u30fc\u30af\u3092\u7dd1(\u6d3b\u6027\u5206\u5b50)\u3001\u305d\u3057\u3066\u3001decoys.final.ldb\u306e\u5de6\u5074\u306e\u30de\u30fc\u30af\u3092\u8d64(\u30c7\u30b3\u30a4\u5206\u5b50)\u306b\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\u6b21\u306b\u3001\u8d64\u56db\u89d2\u5185\u306e\u30a2\u30a4\u30b3\u30f3\u3092\u62bc\u3059\u3053\u3068\u3067\u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u304c\u30b9\u30bf\u30fc\u30c8\u3057\u307e\u3059\u3002\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u304c\u7d42\u308f\u308b\u307e\u3067\u3057\u3070\u3089\u304f\u5f85\u3061\u307e\u3059\u3002<\/p>\n\n\n\n

\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u7d42\u4e86\u5f8c\u3001\u7dd1\u56db\u89d2\u5185\u306e\u30a2\u30a4\u30b3\u30f3\u3092\u62bc\u3059\u3053\u3068\u3067\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u7cbe\u5ea6\u306e\u8a55\u4fa1\u3092AUC\u3001EF\u306b\u3088\u308a\u5b9f\u65bd\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"

<\/figcaption><\/figure>\n\n\n\n

\u6b8b\u5ff5\u306a\u304c\u3089\u30d2\u30c3\u30c8\u5316\u5408\u7269\u306f\u30bc\u30ed\u3067\u3057\u305f\u3002\u3055\u3059\u304c\u306b\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u3092\u69cb\u6210\u3059\u308b8\u500b\u306eFeature\u3092\u5168\u3066\u6e80\u305f\u3059\u5206\u5b50\u306f\u7121\u3044\u3088\u3046\u3067\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u305d\u3053\u3067\u3001Hide advanced options\u3092\u8868\u793a\u3057\u3001Max. number of omitted features (\u8d64\u56db\u89d2)\u30922\u3068\u3057\u307e\u3059\u3002\u3053\u308c\u3067\u5c11\u306a\u304f\u3068\u30826\u500b\u306eFeature\u304c\u6e80\u305f\u3055\u308c\u308c\u3070\u30d2\u30c3\u30c8\u3059\u308b\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

AUC(100%)\u304c0.55\u3068\u306a\u308a\u82e5\u5e72\u6539\u5584\u3055\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u6700\u5f8c\u306b\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u306e\u4fee\u6b63\u3068\u8a2d\u5b9a\u306e\u5909\u66f4\u3092\u884c\u3044\u307e\u3059\u3002\u8d64\u77e2\u5370\u3067\u793a\u3059\uff14\u3064\u306eFeature\u3092\u30aa\u30d7\u30b7\u30e7\u30f3\u3068\u3057\u307e\u3059([Pharmacophore]\u2192[Mark Features as Optinal])\u3002\u305d\u3057\u3066\u9752\u77e2\u5370\u306eFeature\u3092delete\u30ad\u30fc\u3067\u524a\u9664\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\u3053\u306e\u64cd\u4f5c\u306b\u3088\u308a\u3001\u5c11\u306a\u304f\u3068\u30823\u3064\u306eFeature\u306f\u6e80\u305f\u3059\u5fc5\u8981\u304c\u3042\u308b\u304c\u3001\u6b8b\u308a\u306eFeature\u306b\u5bfe\u3057\u3066\u306f\u30de\u30c3\u30c1\u3059\u308c\u3070\u30b9\u30b3\u30a2\u306b\u52a0\u7b97\u3055\u308c\u308b\u3053\u3068\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n

PARP1\u306f\u3001NAD\u3092ADP\u30ea\u30dc\u30fc\u30b9\u3068\u30cb\u30b3\u30c1\u30f3\u30a2\u30df\u30c9\u306b\u5206\u89e3\u3059\u308b\u9175\u7d20\u3067\u3059\u3002\u3053\u306e\uff13\u3064\u306eFeature\u306f\u30cb\u30b3\u30c1\u30f3\u30a2\u30df\u30c9\u306b\u76f8\u5f53\u3059\u308b\u90e8\u5206\u3067\u3059\u306e\u3067\u3001\u30aa\u30d7\u30b7\u30e7\u30f3\u306b\u306f\u3057\u307e\u305b\u3093\u3067\u3057\u305f\u3002\u3053\u3053\u3067\u4fee\u6b63\u3057\u305f\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u3092\u7528\u3044\u3066\u3001\u3053\u308c\u307e\u3067\u3068\u540c\u3058\u624b\u9806\u306b\u3088\u308a\u30d0\u30fc\u30c1\u30e3\u30eb\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u3092\u5b9f\u65bd\u3057\u307e\u3059\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

AUC(100%)\u304c0.84\u3001EF(1%)\u304c33.5\u3068\u5927\u5e45\u306b\u6027\u80fd\u304c\u6539\u5584\u3055\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u30b9\u30b3\u30a2\u30c8\u30c3\u30d7\u306e\u5316\u5408\u7269\u306f\u6d3b\u6027\u5316\u5408\u7269\u306e\uff11\u3064\u3067\u3042\u308b\u4e0a\u56f3\u306e\u5316\u5408\u7269\u3067\u3057\u305f\u3002\u57fa\u8cea\u306e\u60c5\u5831\u3001\u7121\u8996\u3067\u304d\u308bFeature\u6570\u3001\u305d\u3057\u3066\u30aa\u30d7\u30b7\u30e7\u30f3\u7b49\u3092\u5229\u7528\u3059\u308b\u3053\u3068\u3067\u3001\u5358\u72ec\u306e\u7d50\u6676\u69cb\u9020\u304b\u3089\u69cb\u7bc9\u3057\u305f\u30d5\u30a1\u30fc\u30de\u30b3\u30d5\u30a9\u30a2\u3067\u3082\u826f\u3044\u6027\u80fd\u3092\u51fa\u3059\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

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