{"id":69819,"date":"2026-11-14T21:51:17","date_gmt":"2026-11-14T13:51:17","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=69819"},"modified":"2026-11-14T21:51:17","modified_gmt":"2026-11-14T13:51:17","slug":"autodock-vina-seed-exhaustiveness-poses-1iep","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/autodock-vina-seed-exhaustiveness-poses-1iep\/","title":{"rendered":"AutoDock Vina \u5bf9\u63a5\u5b9e\u8dd1\uff0c\u540c\u4e00\u914d\u4f53\u4e3a\u4ec0\u4e48\u4e00\u6b21\u5f97 \u22127.64\uff0c\u53e6\u4e00\u6b21\u5f97 \u221213.28\uff1f"},"content":{"rendered":"
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\u9762\u5bf9\u4e00\u5f20\u5bf9\u63a5\u6392\u540d\u8868\uff0c\u6700\u5bb9\u6613\u8df3\u8fc7\u7684\u662f\u6700\u524d\u9762\u90a3\u4e00\u6b65\u3002\u540c\u4e00\u4e2a\u914d\u4f53\u3001\u540c\u4e00\u4e2a\u53d7\u4f53\u3001\u540c\u4e00\u4e2a\u53e3\u888b\uff0c\u518d\u7b97\u4e00\u6b21\uff0c\u80fd\u5426\u627e\u5230\u76f8\u8fd1\u7684\u59ff\u52bf\uff1f\u6211\u4eec\u7528 AutoDock Vina \u7684\u5b98\u65b9\u6559\u5b66\u4f53\u7cfb\u505a\u4e86\u56db\u6b21\u521a\u6027\u53d7\u4f53\u5bf9\u63a5\u3002\u4e00\u6b21\u4f4e\u5f3a\u5ea6\u641c\u7d22\u7ed9\u51fa\u7684\u7b2c\u4e00\u540d\u4e0e\u53e6\u4e00\u6b21\u76f8\u8ddd\u5341\u4e8c\u57c3\u4ee5\u4e0a\uff0c\u800c\u5728\u8f83\u9ad8\u641c\u7d22\u5f3a\u5ea6\u4e0b\uff0c\u4e24\u6b21\u7b2c\u4e00\u540d\u7684\u8ddd\u79bb\u4e0d\u5230\u4e00\u57c3\u3002\u8fd9\u4e9b\u6570\u503c\u90fd\u662f\u4e00\u6b21\u5c0f\u89c4\u6a21\u590d\u73b0\u7684\u7ed3\u679c\u3002\u4e0b\u9762\u7528\u5b83\u4eec\u8bf4\u660e\u600e\u6837\u4ece\u8f93\u5165\u3001\u641c\u7d22\u548c\u8f93\u51fa\u4e09\u5934\u6838\u8d26\uff0c\u518d\u51b3\u5b9a\u865a\u62df\u7b5b\u9009\u6392\u5e8f\u503c\u4e0d\u503c\u5f97\u5f80\u4e0b\u8ffd\u3002<\/p>\n

\u5148\u56fa\u5b9a\u53d7\u4f53\u3001\u914d\u4f53\u548c\u53e3\u888b\uff0c\u518d\u6bd4\u8f83\u641c\u7d22\u53c2\u6570<\/h2>\n

\u672c\u4f8b\u9009\u7528\u6559\u7a0b\u4e2d\u4ee5\u6676\u4f53\u7ed3\u6784 1IEP \u4e3a\u57fa\u7840\u51c6\u5907\u7684 c-Abl \u6fc0\u9176\u53d7\u4f53\u548c\u914d\u4f53\u4f0a\u9a6c\u66ff\u5c3c\u3002\u76f4\u63a5\u53d6\u5f97\u4f5c\u8005\u51c6\u5907\u597d\u7684\u4e24\u4e2a PDBQT \u6587\u4ef6\u4e0e\u5bf9\u63a5\u76d2\u914d\u7f6e\uff0c\u56fa\u5b9a\u7248\u672c\u5e76\u8bb0\u5f55\u6587\u4ef6\u6821\u9a8c\u503c\u3002\u8fd9\u6837\u56db\u6b21\u8fd0\u884c\u516c\u7528\u540c\u4e00\u5957\u5750\u6807\u3001\u539f\u5b50\u7c7b\u578b\u3001\u7535\u8377\u548c\u53ef\u65cb\u8f6c\u952e\u5b9a\u4e49\uff0c\u5dee\u5f02\u66f4\u5bb9\u6613\u8ffd\u5230\u641c\u7d22\u672c\u8eab\u3002\u82e5\u6362\u6210\u81ea\u5df1\u7684\u7814\u7a76\u5bf9\u8c61\uff0c\u5e94\u5148\u68c0\u67e5\u914d\u4f53\u7684\u4ef7\u6001\u548c\u8d28\u5b50\u5316\u5f62\u5f0f\u3001\u53d7\u4f53\u7684\u94fe\u4e0e\u8f85\u56e0\u5b50\u53d6\u820d\uff0c\u4ee5\u53ca\u5df2\u77e5\u914d\u4f53\u6240\u5728\u53e3\u888b\u662f\u5426\u88ab\u6b63\u786e\u4fdd\u7559\u3002\u4e00\u4efd\u80fd\u88ab\u7a0b\u5e8f\u8bfb\u53d6\u7684\u6587\u4ef6\uff0c\u5e76\u4e0d\u4fdd\u8bc1\u5b83\u63cf\u8ff0\u7684\u662f\u5b9e\u9a8c\u6761\u4ef6\u4e0b\u60f3\u7814\u7a76\u7684\u5316\u5b66\u7269\u79cd\u3002\u5b98\u65b9 1IEP \u5bf9\u63a5\u6559\u7a0b<\/a><\/p>\n

\u76d2\u5b50\u4e2d\u5fc3\u4e3a\u4e09\u7ef4\u5750\u6807 15.190\u300153.903\u300116.917\uff0c\u4e09\u6761\u8fb9\u957f\u90fd\u662f\u4e8c\u5341\u57c3\u3002\u5bf9\u63a5\u76d2\u524d\u4e09\u4e2a\u6570\u662f\u4e2d\u5fc3\uff0c\u540e\u4e09\u4e2a\u6570\u662f\u6cbf\u4e09\u8f74\u7684\u5b8c\u6574\u8de8\u5ea6\uff0c\u5bb9\u6613\u4e0e\u67d0\u4e9b\u7f51\u683c\u5de5\u5177\u4f7f\u7528\u7684\u683c\u70b9\u6570\u6216\u534a\u5f84\u6df7\u6dc6\u3002\u68c0\u67e5\u65f6\u5c06\u76d2\u5b50\u548c\u5171\u6676\u914d\u4f53\u53e0\u5728\u540c\u4e00\u4e2a\u53d7\u4f53\u5750\u6807\u7cfb\u91cc\uff0c\u65e2\u770b\u914d\u4f53\u6709\u6ca1\u6709\u843d\u5728\u76d2\u5185\uff0c\u4e5f\u770b\u8de8\u51fa\u53e3\u7684\u67d4\u6027\u90e8\u5206\u662f\u5426\u6709\u7a7a\u95f4\u8f6c\u52a8\u3002\u82e5\u53d7\u4f53\u4e0e\u76d2\u914d\u7f6e\u66fe\u5206\u522b\u5c45\u4e2d\u6216\u65cb\u8f6c\uff0c\u4e2d\u5fc3\u6570\u503c\u4ecd\u7136\u5408\u4e4e\u8bed\u6cd5\uff0c\u5374\u53ef\u80fd\u5df2\u7ecf\u628a\u641c\u7d22\u9001\u5230\u86cb\u767d\u53e6\u4e00\u4fa7\u3002\u4e3a\u4e86\u8ba9\u540c\u4e8b\u80fd\u91cd\u73b0\u8fd9\u4e2a\u6b65\u9aa4\uff0c\u4fdd\u5b58\u5b9e\u9645\u4f7f\u7528\u7684\u76d2\u6587\u4ef6\u6bd4\u5728\u7b14\u8bb0\u91cc\u5199\u201c\u56f4\u7ed5\u6d3b\u6027\u4e2d\u5fc3\u8bbe\u7f6e\u201d\u66f4\u660e\u786e\u3002\u672c\u6b21\u4f7f\u7528\u7684\u4f5c\u8005\u793a\u4f8b\u6587\u4ef6<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u628a\u4e24\u4e2a\u79cd\u5b50\u548c\u4e24\u4e2a\u641c\u7d22\u5f3a\u5ea6\u4ea4\u53c9\u8d77\u6765<\/h2>\n

\u5728 Ubuntu \u5b89\u88c5 AutoDock Vina 1.2.5\uff0c\u4f7f\u7528\u9ed8\u8ba4 Vina \u6253\u5206\uff0c\u4e0d\u542f\u7528\u53d7\u4f53\u67d4\u6027\u3002\u8bbe\u4e00\u4e2a\u6267\u884c\u7ebf\u7a0b\uff0c\u8bf7\u6c42\u6700\u591a\u4e5d\u79cd\u6a21\u5f0f\u3002\u5148\u5c06\u641c\u7d22\u5f3a\u5ea6\u8bbe\u4e3a\u4e00\uff0c\u5206\u522b\u8fd0\u884c\u968f\u673a\u79cd\u5b50\u4e09\u5341\u4e03\u548c\u4e5d\u5341\u4e09\u3002\u518d\u628a\u5f3a\u5ea6\u6539\u4e3a\u516b\uff0c\u4fdd\u6301\u5176\u4ed6\u8f93\u5165\u5e76\u91cd\u590d\u4e24\u4e2a\u79cd\u5b50\u3002\u4e0b\u9762\u7684\u9996\u4f4d\u5206\u6570\u53d6\u81ea\u5404\u6b21\u5199\u51fa\u7684\u6784\u8c61\u6587\u4ef6\uff0c\u5355\u4f4d\u4e3a\u6bcf\u6469\u5c14\u5343\u5361\u3002\u6784\u8c61\u6570\u662f\u5404\u8f93\u51fa\u6587\u4ef6\u5b9e\u9645\u8bb0\u5f55\u7684\u6a21\u578b\u6570\uff0c\u5206\u6570\u53ea\u80fd\u5728\u6b64\u5904\u56fa\u5b9a\u7684\u51c6\u5907\u65b9\u5f0f\u4e0e\u6253\u5206\u51fd\u6570\u4e0b\u89e3\u8bfb\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u641c\u7d22\u5f3a\u5ea6<\/th>\n\u968f\u673a\u79cd\u5b50<\/th>\n\u9996\u4f4d\u5206\u6570<\/th>\n\u6587\u4ef6\u4e2d\u5b9e\u9645\u6784\u8c61\u6570<\/th>\n<\/tr>\n<\/thead>\n
1<\/td>\n37<\/td>\n\u22127.641<\/td>\n1<\/td>\n<\/tr>\n
1<\/td>\n93<\/td>\n\u221213.282<\/td>\n1<\/td>\n<\/tr>\n
8<\/td>\n37<\/td>\n\u221213.242<\/td>\n3<\/td>\n<\/tr>\n
8<\/td>\n93<\/td>\n\u221213.220<\/td>\n3<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u6362\u4e2a\u79cd\u5b50\uff0c\u59ff\u52bf\u5dee\u591a\u5c11\u30021IEP
1IEP \u5b98\u65b9\u6837\u4f8b\u5b9e\u8dd1\uff5c\u56db\u6b21\u641c\u7d22\u5171\u7528\u540c\u4e00\u5957\u53d7\u4f53\u3001\u914d\u4f53\u4e0e\u53e3\u888b\u3002<\/figcaption><\/figure>\n

\u4f4e\u5f3a\u5ea6\u4e0b\uff0c\u4ec5\u4ea4\u6362\u968f\u673a\u79cd\u5b50\uff0c\u4e24\u4e2a\u9996\u4f4d\u5206\u6570\u5c31\u76f8\u5dee 5.641\u3002\u5f3a\u5ea6\u63d0\u9ad8\u5230\u516b\u540e\uff0c\u4e24\u4e2a\u9996\u4f4d\u5206\u6570\u76f8\u5dee\u7ea6 0.022\u3002\u4e0d\u8fc7\u56db\u6b21\u91cc\u6570\u503c\u6700\u8d1f\u7684\u4e00\u6b21\u4ecd\u51fa\u73b0\u5728\u4f4e\u5f3a\u5ea6\u641c\u7d22\u3002\u589e\u52a0\u641c\u7d22\u5f3a\u5ea6\u7ed9\u4e86\u7a0b\u5e8f\u66f4\u591a\u673a\u4f1a\u627e\u5230\u80fd\u91cf\u8f83\u4f4e\u7684\u533a\u57df\uff0c\u5e76\u4e0d\u4fdd\u8bc1\u6bcf\u4e2a\u968f\u673a\u79cd\u5b50\u7684\u9996\u4f4d\u5206\u6570\u90fd\u6bd4\u4e4b\u524d\u66f4\u4f4e\u3002\u5b9e\u9645\u7b5b\u9009\u82e5\u53ea\u770b\u5230\u67d0\u4e00\u4e2a\u79cd\u5b50\u6392\u51fa\u7684\u7b2c\u4e00\u540d\uff0c\u53ef\u4ee5\u5148\u505a\u8fd9\u6837\u7684\u91cd\u590d\uff0c\u518d\u51b3\u5b9a\u662f\u5426\u628a\u4e00\u4e2a\u914d\u4f53\u6392\u5728\u53e6\u4e00\u4e2a\u524d\u9762\u3002\u5c24\u5176\u662f\u4e24\u4e2a\u5019\u9009\u53ea\u5dee\u96f6\u70b9\u51e0\u5206\u65f6\uff0c\u8fd8\u8981\u8861\u91cf\u540c\u4e00\u5206\u5b50\u91cd\u590d\u641c\u7d22\u672c\u8eab\u4f1a\u6d6e\u52a8\u591a\u5c11\u3002<\/p>\n

vina --receptor 1iep_receptor.pdbqt --ligand 1iep_ligand.pdbqt \\\r\n  --config 1iep_receptor.box.txt --cpu 1 --seed 37 \\\r\n  --exhaustiveness 8 --num_modes 9 --out e8_s37.pdbqt\r\n# \u4e24\u4e2a\u6587\u4ef6\u91cf\u7684\u662f\u4e0d\u540c\u7684\u4e1c\u897f\uff0c\u5206\u522b\u67e5\u770b\r\ngrep '^MODEL' e8_s37.pdbqt\r\ngrep '^REMARK VINA RESULT' e8_s37.pdbqt\r\n<\/code><\/pre>\n
\u8fd8\u78b0\u5230\u4e00\u4e2a\u5bb9\u6613\u88ab\u6279\u5904\u7406\u811a\u672c\u63a9\u76d6\u7684\u7ec6\u8282\u3002\u5f3a\u5ea6\u516b\u3001\u79cd\u5b50\u4e09\u5341\u4e03\u65f6\uff0c\u7ec8\u7aef\u6253\u5370\u4e5d\u884c\u5019\u9009\uff0c\u8f93\u51fa\u6587\u4ef6\u91cc\u5374\u53ea\u4fdd\u5b58\u4e09\u4efd\u6a21\u578b\u3002\u7b2c\u4e00\u540d\u4e3a\u8d1f\u5341\u4e09\u70b9\u4e8c\u56db\u4e8c\uff0c\u7b2c\u56db\u540d\u5728\u65e5\u5fd7\u4e2d\u7ea6\u4e3a\u8d1f\u4e5d\u70b9\u516b\u4e03\u4e00\uff0c\u4e24\u8005\u76f8\u5dee\u5df2\u7ecf\u8d85\u8fc7\u9ed8\u8ba4\u5199\u51fa\u80fd\u91cf\u7a97\u53e3\u7684\u4e09\u3002\u56e0\u800c\u5e94\u6e05\u70b9\u8f93\u51fa\u6587\u4ef6\u91cc\u7684\u6a21\u578b\u6bb5\uff0c\u518d\u6309\u5b9e\u9645\u5b58\u5728\u7684\u6784\u8c61\u63d0\u53d6\u5750\u6807\u3002\u5982\u679c\u8868\u683c\u9884\u5148\u521b\u5efa\u4e5d\u884c\uff0c\u53c8\u628a\u6ca1\u5199\u51fa\u7684\u6784\u8c61\u8865\u96f6\uff0c\u90a3\u4e9b\u96f6\u7ecf\u540e\u7eed\u805a\u5408\u4fbf\u53ef\u80fd\u88ab\u8bef\u5f53\u6210\u771f\u5b9e\u7ed3\u679c\u3002\u4f5c\u8005\u5bf9\u8f93\u51fa\u6a21\u5f0f\u6570\u548c\u80fd\u91cf\u7a97\u53e3\u7684\u8bf4\u660e<\/a><\/p>\n
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