{"id":2712,"date":"2022-03-05T14:54:22","date_gmt":"2022-03-05T06:54:22","guid":{"rendered":"http:\/\/139.9.1.231\/?p=2712"},"modified":"2022-03-30T17:24:30","modified_gmt":"2022-03-30T09:24:30","slug":"aifenzi","status":"publish","type":"post","link":"http:\/\/139.9.1.231\/index.php\/2022\/03\/05\/aifenzi\/","title":{"rendered":"AI\u5236\u836f \uff1a \u5206\u5b50\u5bf9\u63a5"},"content":{"rendered":"\n\n\n

\u4efb\u52a1\uff1a<\/p>\n\n\n\n

1\u3001\u5b89\u88c5\u5b66\u4e60yutobe\u4e0a\u9762\u7684\u8f6f\u4ef6<\/p>\n\n\n\n

https:\/\/www.youtube.com\/watch?v=Sux91FJ3Xe8&t=629s<\/a><\/p>\n\n\n\n

2\u3001\u8dd1\u901a\u8bba\u6587\u4ee3\u7801<\/p>\n\n\n\n

https:\/\/www.youtube.com\/watch?v=Sux91FJ3Xe8&t=629s<\/a><\/p>\n\n\n\n

<\/p>\n\n\n\n

Pymol\u7b80\u4ecb<\/h2>\n\n\n\n

Pymol\u662f\u4e00\u6b3e\u64cd\u4f5c\u7b80\u5355\uff0c\u529f\u80fd\u5f3a\u5927\u7684\u5206\u5b50\u4ee5\u53ca\u86cb\u767d\u7684\u53ef\u89c6\u5316\u8f6f\u4ef6\uff0c\u7531\u859b\u5b9a\u8c14\u516c\u53f8\u7814\u53d1\uff0c\u79d1\u7814\u4eba\u5458\u53ef\u4ee5\u4ece\u5b98\u7f51\u7533\u8bf7\u6700\u65b0\u6559\u80b2\u7248\u672c\uff0c\u540c\u65f6pymo\u7684\u5f00\u6e90\u7248\uff08https:\/\/github.com\/schrodinger\/pymol-open-source<\/a>\uff09\uff0c\u53ef\u4ee5\u76f4\u63a5\u4ece\u7f51\u7ad9\u4e0a\u4e0b\u8f7d\uff0c\u4f46\u662f\u7248\u672c\u8f83\u8001\u3002\u6240\u4ee5\uff0c\u6839\u636e\u9700\u6c42\u9009\u62e9\u7248\u672c\u8fdb\u884c\u4e0b\u8f7d\u3002 \u8bf4\u660e\uff1a https:\/\/cloud.tencent.com\/developer\/article\/1785088<\/a><\/p>\n\n\n\n

Pymol\u5165\u95e8\u6559\u7a0b\uff1a<\/h1>\n\n\n\n

http:\/\/pymol.chenzhaoqiang.com\/intro\/startManual.html<\/a><\/p>\n\n\n\n

\u5206\u5b50\u5bf9\u63a5\u6559\u7a0b<\/h1>\n\n\n\n

1\u3001<\/p>\n\n\n\n

https:\/\/cloud.tencent.com\/developer\/inventory\/15332<\/a><\/p>\n\n\n\n

2\u3001https:\/\/www.bilibili.com\/video\/av466685164?from=search&seid=9870338638011316620&spm_id_from=333.337.0.0<\/a><\/p>\n\n\n\n

vina\u53ea\u8d1f\u8d23\u5bf9\u63a5\uff0cmgltool\u8d1f\u8d23\u63d0\u4f9b\u86cb\u767d\u8d28\u5206\u5b50\u548c\u914d\u4f53\u5206\u5b50\u3002<\/p>\n\n\n\n

\u5148\u7528MGL \u751f\u6210vina\u9700\u8981\u7684pdbqt\u6587\u4ef6<\/p>\n\n\n\n

MGL tools\u7684\u4f5c\u7528\u5c31\u662f\u751f\u6210pdbqt\u6587\u4ef6<\/p>\n\n\n\n

1\u3001\uff1a\u6253\u5f00MGL tools\uff0c\u6253\u5f00\u53d7\u4f53\u86cb\u767d\u7684pdb \uff1afile-\u300bread molecule<\/p>\n\n\n\n

2\u3001\u86cb\u767d\u8d28\u7684pdb\uff08\u6570\u636e\u5e93\uff09\uff1a<\/p>\n\n\n\n

\u5173\u4e8e\u86cb\u767d\u8d28\u7ed3\u6784\u7684PDB\u6587\u4ef6\uff0c\u505a\u5206\u5b50\u5bf9\u63a5\uff0c\u4f30\u8ba1\u5927\u5bb6\u90fd\u77e5\u9053PDB\u8fd9\u4e2a\u86cb\u767d\u8d28\u6570\u636e\u5e93<\/a>\u5566\u3002\u8fd9\u91cc\u7b80\u5355\u7684\u4ecb\u7ecd\u4e00\u4e0b\u3002<\/p>\n\n\n\n

\u86cb\u767d\u8d28\u7684\u4e09\u7ea7\u7ed3\u6784\u662f\u6307\u6574\u6761\u591a\u80bd\u94fe\u7684\u4e09\u7ef4\u7a7a\u95f4\u7ed3\u6784\uff0c\u4e5f\u5c31\u662f\u5305\u62ec\u78b3\u9aa8\u67b6\u548c\u4fa7\u94fe\u5728\u5185\u7684\u6240\u6709\u539f\u5b50\u7684\u7a7a\u95f4\u6392\u5217\u3002\u7b2c\u4e00\u4e2a\u86cb\u767d\u8d28\u7684\u4e09\u7ef4\u7a7a\u95f4\u7ed3\u6784\u4e8e 1958 \u5e74\u7528 X-\u5c04\u7ebf\u884d\u5c04\u6cd5\uff08X-ray Crystallography\uff09\u6d4b\u5b9a\u3002\u8fd9\u79cd\u65b9\u6cd5\u76ee\u524d\u4ecd\u7136\u662f\u83b7\u53d6\u86cb\u767d\u8d28\u4e09\u7ea7\u7ed3\u6784\u7684\u4e3b\u8981\u65b9\u6cd5\u3002PDB \u6570\u636e\u5e93\u4e2d\u7edd\u5927\u591a\u6570\u86cb\u767d\u8d28\u7ed3\u6784\u90fd\u662f\u7528\u8fd9\u79cd\u65b9\u6cd5\u6d4b\u5b9a\u7684\u3002\u53e6\u4e00\u4e2a\u6d4b\u5b9a\u86cb\u767d\u8d28\u4e09\u7ef4\u7a7a\u95f4\u7ed3\u6784\u7684\u65b9\u6cd5\u662f\u6838\u78c1\u5171\u632f\u6cd5\uff08Nuclear Magnetic Resonance, NMR\uff09\u3002\u65e0\u6cd5\u7ed3\u6676\u7684\u86cb\u767d\u8d28\uff0c\u53ef\u4ee5\u5229\u7528\u6838\u78c1\u5171\u632f\u6cd5\u5728\u6db2\u4f53\u73af\u5883\u4e2d\u8fdb\u884c\u7ed3\u6784\u6d4b\u5b9a\u3002\u4f46\u662f\u6838\u78c1\u5171\u632f\u6cd5\u53ea\u80fd\u7528\u4e8e\u8d28\u91cf\u5c0f\u4e8e 70 \u5343\u9053\u5c14\u987f\u7684\u5206\u5b50\uff0c\u5927\u7ea6\u5bf9\u5e94 200 \u4e2a\u6c28\u57fa\u9178\u7684\u957f\u5ea6\u3002\u9664\u6b64\u4e4b\u5916\uff0c\u8fd8\u6709\u4e00\u4e9b\u4e0d\u592a\u5e38\u7528\u7684\u65b9\u6cd5\u4e5f\u53ef\u4ee5\u6d4b\u5b9a\u5206\u5b50\u7684\u4e09\u7ef4\u7a7a\u95f4\u7ed3\u6784\uff0c\u6bd4\u5982\u51b7\u51bb\u7535\u5b50\u663e\u5fae\u955c\u6280\u672f\uff08Cyro-Electron Microscopy\uff09\u3002\u65e0\u8bba\u7528\u4ec0\u4e48\u65b9\u6cd5\u6d4b\u5b9a\u7684\u7a7a\u95f4\u7ed3\u6784\uff0c\u90fd\u8981\u63d0\u4ea4\u5230 PDB \u6570\u636e\u5e93\u3002\u6240\u4ee5\u6211\u4eec\u83b7\u53d6\u86cb\u767d\u8d28\u4e09\u7ea7\u7ed3\u6784\u6700\u76f4\u63a5\u7684\u529e\u6cd5\u5c31\u662f\u53bbPDB \u641c\u7d22\uff08http:\/\/www.rcsb.org\/<\/a>\uff09\u3002 \u4ecePDB\u9996\u9875\u7684\u641c\u7d22\u6761\u91cc\uff0c\u53ef\u4ee5\u901a\u8fc7\u641c\u7d22PDB ID\u3001\u5206\u5b50\u540d\u79f0\u3001\u4f5c\u8005\u59d3\u540d\u7b49\u5173\u952e\u8bcd\u6765\u67e5\u627e\u86cb\u767d\u8d28\u4e09\u7ea7\u7ed3\u6784\u3002\u6b64\u5916\uff0c\u5229\u7528\u9ad8\u7ea7\u641c\u7d22\u5de5\u5177\uff0c\u53ef\u4ee5\u901a\u8fc7\u5e8f\u5217\u76f8\u4f3c\u6027\u641c\u7d22\u83b7\u5f97\u4e0e\u8f93\u5165\u5e8f\u5217\u5728\u5e8f\u5217\u6c34\u5e73\u4e0a\u76f8\u4f3c\u7684\u86cb\u767d\u8d28\u7684\u4e09\u7ea7\u7ed3\u6784\u3002\u641c\u7d22\u65b9\u6cd5\u9009 BLAST\uff0c\u8f93\u5165\u5e8f\u5217\uff0c\u70b9\u51fb\u201cResult Count\u201d\u3002\u8fd9\u91cc\u4e0d\u8be6\u7ec6\u4ecb\u7ecd\uff0c\u56e0\u4e3a\u6211\u4eec\u505a\u5206\u5b50\u5bf9\u63a5\uff0c\u901a\u5e38\u86cb\u767d\u540d\u79f0\u662f\u5df2\u77e5\u7684\u3002\u6211\u4eec\u91cd\u70b9\u4ecb\u7ecd\u600e\u4e48\u9009\u62e9\u5408\u9002\u7684\u86cb\u767d\u7ed3\u6784\u6587\u4ef6\u3002 \u6bd4\u5982\u6211\u4eec\u641c\u7d22PI3K\u8fd9\u4e2a\u86cb\u767d\uff0c\u76f4\u63a5\u5728\u641c\u7d22\u680f\u641c\u7d22\uff0c\u7ed3\u679c\u662f\u6709\u5f88\u591a\u7684\u3002\u53ef\u4ee5\u770b\u5230\u6709393\u4e2a\u7ed3\u6784\u4fe1\u606f\u3002\u9996\u5148\u6211\u4eec\u53ef\u4ee5\u901a\u8fc7\u5de6\u8fb9\u7684\u680f\u8fdb\u884c\u7b5b\u9009\uff0c\u6bd4\u5982\u7269\u79cd\u4fe1\u606f\uff0c\u6211\u4eec\u9009\u62e9\u4eba\u3002\u5f53\u7136\uff0c\u7ed3\u679c\u7684\u663e\u793a\u6392\u5e8f\u53ef\u901a\u8fc7\u7ed3\u679c\u4e0a\u9762\u7684\u9009\u9879\u5361\u8fdb\u884c\u9009\u62e9\u4e0d\u540c\u7684\u6392\u5e8f\u65b9\u5f0f\u3002\u6211\u4eec\u7b5b\u9009\u5408\u9002\u7684\u86cb\u767d\u7ed3\u6784\uff0c\u5e38\u7528Score\u8fd9\u4e2a\u9009\u9879.\u6211\u4eec\u9009\u62e9\u5206\u8fa8\u7387\u8f83\u597d\u7684\u5728\u524d\u3002\u8fd9\u91cc\u76840.9\u00c5\uff0c\u00c5\u662f\u5149\u6ce2\u957f\u5ea6\u548c\u5206\u5b50\u76f4\u5f84\u7684\u5e38\u7528\u8ba1\u91cf\u5355\u4f4d\uff0c\u503c\u8d8a\u5c0f\uff0c\u5206\u8fa8\u7387\u8d8a\u9ad8\uff0c\u7ed3\u6784\u8d8a\u51c6\u786e\u3002\u9875\u9762\u5f80\u4e0b\u62c9\uff0c\u53ef\u4ee5\u770b\u89c1\u8fd9\u4e2a\u503c\u8d8a\u6765\u8d8a\u5927\uff0c\u6211\u4eec\u4f18\u5148\u9009\u62e9\u503c\u5c0f\u7684\u3002\u6211\u4eec\u53ef\u4ee5\u4ece\u9875\u9762\u91cc\u9762\u770b\u89c1\u4e00\u4e0b\u57fa\u672c\u4fe1\u606f\uff0c\u6bd4\u5982\u65b9\u6cd5\uff0c\u7269\u79cd\u4ee5\u53ca\u88ab\u89e3\u6790\u7684\u65f6\u95f4\u7b49\u3002\u8fd9\u91cc5GJI\u8fd9\u4e2a\u7ed3\u6784\u83b7\u53d6\u7684\u65b9\u6cd5\u5c31\u662fX-RAY\u3002\u6211\u4eec\u70b9\u51fb\u8fd9\u4e2a\u86cb\u767d\uff0c\u8fdb\u5165\u540e\u53ef\u4ee5\u770b\u89c1\u8be6\u7ec6\u7684\u4fe1\u606f\u3002\u7136\u540e\u6211\u4eec\u8fd8\u8981\u770b\u8fd9\u4e2a\u86cb\u767d\u7684\u63cf\u8ff0\u662f\u4e0d\u662f\u6211\u4eec\u60f3\u8981\u7684\u86cb\u767d\uff0c\u4ece\u8fd9\u91cc\u9762\u611f\u89c9\u770b\u8d77\u6765\u6bd4\u8f83\u8d39\u52b2\u3002\u8fd9\u91cc\u6211\u4eec\u501f\u52a9uniprot\u8fd9\u4e2a\u6570\u636e\u5e93\u6765\u9009\u62e9\u662f\u6bd4\u8f83\u65b9\u4fbf\u7684\u3002\u8fd9\u91cc\u7b80\u5355\u4ecb\u7ecd\u4e00\u4e0b\u8fd9\u4e2a\u6570\u636e\u5e93\uff0c\u53ef\u80fd\u6709\u7684\u540c\u5b66\u662f\u7b2c\u4e00\u6b21\u77e5\u9053\u3002\u7ffb\u4e86\u591a\u5e74\u524d\u7684\u7b14\u8bb0\uff0c\u7c98\u8d34\u5728\u4e0b\u9762\u3002 UniProt \u6570\u636e\u5e93\u6709\u4e09\u4e2a\u5c42\u6b21\u3002<\/p>\n\n\n\n

\u7b2c\u4e00\u5c42\u53eb UniParc\uff0c\u6536\u5f55\u4e86\u6240\u6709 UniProt \u6570\u636e\u5e93\u5b50\u5e93\u4e2d\u7684\u86cb\u767d\u8d28\u5e8f\u5217\uff0c\u91cf\u5927\uff0c\u7c97\u7cd9\u3002<\/p>\n\n\n\n

\u7b2c\u4e8c\u5c42\u662f UniRef\uff0c\u4ed6\u5f52\u7eb3\u4e86 UniProt \u51e0\u4e2a\u4e3b\u8981\u6570\u636e\u5e93\u5e76\u4e14\u662f\u5c06\u91cd\u590d\u5e8f\u5217\u53bb\u9664\u540e\u7684\u6570\u636e\u5e93\u3002<\/p>\n\n\n\n

\u7b2c\u4e09\u5c42\u662f UniProtKB\uff0c\u4ed6\u6709\u8be6\u7ec6\u6ce8\u91ca\u5e76\u4e0e\u5176\u4ed6\u6570\u636e\u5e93\u6709\u94fe\u63a5\uff0c\u5206\u4e3a UniProtKB \u4e0b\u7684 Swiss-Prot\u548c UniProtKB \u4e0b\u7684 TrEMBL \u6570\u636e\u5e93\u3002<\/p>\n\n\n\n

\u5173\u7cfb\u7a0d\u6709\u70b9\u590d\u6742\uff0c\u4f46\u5b9e\u9645\u4e0a\u6211\u4eec\u6700\u5e38\u7528\u7684\u5c31\u662f UniProtKB\u4e0b\u7684 Swiss-Prot \u6570\u636e\u5e93\u3002<\/p>\n\n\n\n

\u4ece UniProt \u6570\u636e\u5e93\u67e5\u770b\u4e00\u6761\u86cb\u767d\u8d28\u5e8f\u5217\uff08http:\/\/www.uniprot.org\/<\/a>\uff09\u3002\u5728UniProt\u6570\u636e\u5e93\u7684\u9996\u9875\u4e0a\u6709\u4e00\u4e2a\u5173\u4e8e UniProtKB \u6570\u636e\u5e93\u7684\u7edf\u8ba1\u8868\u3002\u53ef\u4ee5\u770b\u5230\uff0cTrEMBL \u6570\u636e\u5e93\u91cc\u5b58\u50a8\u7684\u5e8f\u5217\u6570\u91cf\u8fdc\u8fdc\u5927\u4e8e Swiss-Prot \u4e2d\u7684\u3002\u7edf\u8ba1\u8868\u91cc\u6e05\u695a\u7684\u5199\u7740\uff1aTrEMBL \u662f\u81ea\u52a8\u6ce8\u91ca\u7684\uff0c\u6ca1\u6709\u7ecf\u8fc7\u68c0\u67e5\uff0c\u800c Swiss-Prot \u662f\u4eba\u5de5\u6ce8\u91ca\u7684\uff0c\u5e76\u4e14\u7ecf\u8fc7\u68c0\u67e5\u3002<\/p>\n\n\n\n

\u7136\u540e\u70b9\u51fb\u4e0b\u8f7d\u6587\u4ef6\u5c31\u53ef\u4ee5\u76f4\u63a5\u4e0b\u8f7dPDB\u683c\u5f0f\u7684\u86cb\u767d\u7ed3\u6784\u6587\u4ef6\u3002\u4e0b\u8f7d\u7684PDB\u6587\u4ef6\u53ef\u4ee5\u7528pymol\u6216\u8005VMD\u89c2\u5bdf\u7ed3\u6784\u3002\u80fd\u591f\u5b9e\u73b0\u86cb\u767d\u8d28\u4e09\u7ef4\u7ed3\u6784\u53ef\u89c6\u5316\u7684\u8f6f\u4ef6\u975e\u5e38\u591a\u3002\u6bd4\u4e13\u4e1a\u7ea7\u7684PyMOL\uff08https:\/\/pymol.org\/2\/<\/a>\uff09\u3002\u8fd9\u4e2a\u8f6f\u4ef6\u5df2\u7ecf\u88ab\u4e16\u754c\u4e0a\u8457\u540d\u7684\u751f\u7269\u533b\u836f\u8f6f\u4ef6\u516c\u53f8\u201c\u859b\u5b9a\u8c14\u516c\u53f8\uff08Schr\u00f6dinger\uff09\u201d\u6536\u8d2d\u3002\u8fd9\u79cd\u4e13\u4e1a\u7ea7\u7684\u53ef\u89c6\u5316\u8f6f\u4ef6\u4e0d\u4ec5\u80fd\u591f\u505a\u51fa\u975e\u5e38\u6f02\u4eae\u7684\u56fe\u7247\uff0c\u5b83\u8fd8\u6709\u5f3a\u5927\u7684\u63d2\u4ef6\u652f\u6301\u5404\u79cd\u5404\u6837\u7684\u86cb\u767d\u8d28\u7ed3\u6784\u5206\u6790\uff0c\u8fd9\u6b3e\u8f6f\u4ef6\u9700\u8981\u8d2d\u4e70\uff0c\u5982\u679c\u4f60\u53d1\u8868\u7684\u6587\u7ae0\u91cc\u63d0\u5230\u67d0\u4e9b\u5185\u5bb9\u662f\u4f7f\u7528PyMOL\u5236\u4f5c\u7684\uff0c\u800c\u6587\u7ae0\u4e2d\u6240\u6709\u4f5c\u8005\u548c\u4f5c\u8005\u5355\u4f4d\u90fd\u6ca1\u6709PyMOL\u7684\u8d2d\u4e70\u8bb0\u5f55\u7684\u8bdd\uff0c\u4f60\u53ef\u80fd\u4f1a\u9762\u4e34\u859b\u5b9a\u8c14\u516c\u53f8\u7684\u8ffd\u8d23\u3002 \u5982\u679c\u8981\u5bf9\u63a5\u7684\u86cb\u767d\u6ca1\u6709\u7ed3\u6784\uff0c\u6211\u4eec\u53c8\u8981\u5bf9\u63a5\uff0c\u90a3\u5c31\u53ea\u80fd\u662f\u81ea\u5df1\u901a\u8fc7\u8f6f\u4ef6\u9884\u6d4b\u4e86\u3002\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\u7684\u65b9\u6cd5\u6709\u4ece\u5934\u8ba1\u7b97\u6cd5\uff0c\u540c\u6e90\u5efa\u6a21\u6cd5\uff0c\u7a7f\u7ebf\u6cd5\u548c\u7efc\u5408\u6cd5\u3002\u5e38\u7528\u7684\u662f\u540c\u6e90\u5efa\u6a21\u6cd5\uff0cSWISS-MODEL\uff08www.swissmodel.expasy.org<\/a>\uff09\u5c31\u662f\u4e00\u6b3e\u7528\u540c\u6e90\u5efa\u6a21\u6cd5\u9884\u6d4b\u86cb\u767d\u8d28\u4e09\u7ea7\u7ed3\u6784\u7684\u5168\u81ea\u52a8\u8f6f\u4ef6\uff0c\u8fd9\u91cc\u4e0d\u8be6\u7ec6\u4ecb\u7ecd\u4e86\uff0c\u9884\u6d4b\u7684\u6a21\u578b\u8fd8\u8981\u6d89\u53ca\u6a21\u578b\u597d\u574f\u7684\u8bc4\u4ef7\uff0c\u540e\u7eed\u6709\u65f6\u95f4\uff0c\u518d\u4ecb\u7ecd\u86cb\u767d\u8d28\u4e09\u7ea7\u7ed3\u6784\u7684\u9884\u6d4b\u3002<\/p>\n\n\n\n

\u63a5\u4e0b\u6765\u6211\u4eec\u6253\u5f00AutoDockTools(ADT)\uff0c\u6253\u5f00\u6211\u4eec\u524d\u9762\u4fdd\u5b58\u7684\u6587\u4ef61E8Y_PYMOL.pdb<\/p>\n\n\n\n

\u5220\u9664\u6c34\u5206\u5b50\u548c\u5176\u4ed6\u914d\u4f53\uff0c\u5e38\u89c4\u64cd\u4f5c\u4e0d\u7528\u89e3\u91ca<\/p>\n\n\n\n

\u7136\u540e\u8ba1\u7b97\u7535\u8377\u548c\u6dfb\u52a0\u539f\u5b50\u7c7b\u578b<\/p>\n\n\n\n

Edit–Charges–Compute Gasteiger<\/p>\n\n\n\n

Edit–Atoms–Assign AD4 type<\/p>\n\n\n\n

\u5c31\u53ef\u4ee5\u5bfc\u51fa\u6210pbdqt\u683c\u5f0f\u7684\u6587\u4ef6\u4e86<\/p>\n\n\n\n

\u7136\u540e\u53f3\u952e\u5427\u86cb\u767d\u5220\u9664\u6389\uff0c\u5bfc\u5165\u914d\u4f53\u5c0f\u5206\u5b50\uff0c\u968f\u4fbf\u4eceZINC\u4e0b\u4e86\u4e00\u4e2a<\/p>\n\n\n\n

ZINC(http:\/\/zinc.docking.org\/<\/a>) \u8fd8\u6709\u4e00\u4e2a\u6570\u636e\u5e93\u80fd\u4e0b\u8f7dmol2\u683c\u5f0f\u7684\u6587\u4ef6\u3002ZINC)\uff0c\u8fd9\u91cc\u5c31\u4e0d\u4ecb\u7ecd\u4e86\uff0c\u4f60\u8981\u662f\u80fd\u4ece\u4e0a\u9762\u7684\u6570\u636e\u5e93\u4e0b\u8f7d\u5230\u4f60\u914d\u4f53\u5c0f\u5206\u5b50\u7684mol2\u683c\u5f0f\u6587\u4ef6\uff0c\u5c31\u76f4\u63a5\u7528\uff0c\u5982\u679c\u4e0d\u80fd\uff0c\u90a3\u5c31\u662f\u53bbPubChem\u6570\u636e\u5e93(https:\/\/pubchem.ncbi.nlm.nih.gov\/<\/a>)\u4e0b\u8f7dsdf\u6587\u4ef6\uff0c\u7136\u540e\u8fdb\u884c\u8f6c\u6362\uff0c\u8fd9\u4e5f\u662f\u6211\u8fd9\u91cc\u8981\u4ecb\u7ecd\u7684\u3002<\/p>\n\n\n\n

Ligand-input-open<\/p>\n\n\n\n

\u5206\u5b50\u5bf9\u63a5\u6559\u7a0b<\/strong><\/h2>\n\n\n\n

1 \u5206\u5b50\u5bf9\u63a5\u7684\u5de5\u4f5c\u73af\u5883
1.1 \u5bf9\u63a5\u57fa\u672c\u9700\u6c42
\u53d7\u4f53\u7684 pdb \u6587\u4ef6\u3001\u77e5\u9053\u914d\u4f53\u7684\u7ed3\u6784
1.2 \u5bf9\u63a5\u8f6f\u4ef6
\u4f7f\u7528 AutoDock \u8fdb\u884c\u5bf9\u63a5\uff0c\u8be5\u8f6f\u4ef6\u7531 AutoDock \u548c MGLTools \u4e24
\u90e8\u5206\u7ec4\u6210\uff0cAutoDock \u4e3a\u4e3b\u7a0b\u5e8f\uff0c\u4ec5\u63d0\u4f9b\u4e86\u547d\u4ee4\u884c\u63a5\u53e3\uff0c\u800c MGLTools
\u4e2d\u7684 AutoDockTools\uff08ADT\uff09\u53ef\u4ee5\u770b\u4f5c\u662f AutoDock \u7684\u56fe\u5f62\u7528\u6237\u754c\u9762\u3002
\u914d\u4f53\u4f7f\u7528 ChemDraw \u548c Chem3D \u7ed8\u5236\uff0c\u8be5\u8f6f\u4ef6\u4e3a\u6536\u8d39\u8f6f\u4ef6\uff0c\u53ef
\u4f7f\u7528\u5176\u5b83\u514d\u8d39\u7684\u7ed3\u6784\u5f0f\u7ed8\u5236\u5de5\u5177\u8fdb\u884c\u7ed3\u6784\u7ed8\u5236\uff0c\u4f7f\u7528 Open Babel \u8f6c
3D \u7ed3\u6784\u548c\u6587\u4ef6\u683c\u5f0f\u7684\u8f6c\u6362\u3002
\u4f7f\u7528 PyMol \u5f00\u6e90\u7248\u672c\u5bf9\u53d7\u4f53\u86cb\u767d\u7684 pdb \u6587\u4ef6\u8fdb\u884c\u5904\u7406\u3002<\/p>\n\n\n\n

2 \u51c6\u5907\u53d7\u4f53\u3001\u914d\u4f53\u7684 pdbqt \u6587\u4ef6<\/p>\n\n\n\n


AutoDock \u53ea\u63a5\u53d7 pdbqt \u683c \u5f0f \u7684 \u6587 \u4ef6 \uff0c \u6240 \u4ee5 \u9700 \u8981 \u901a \u8fc7
AutoDockTools \u5c06 pdb \u6216\u8005\u5176\u4ed6\u683c\u5f0f\u7684\u6587\u4ef6\u8f6c\u5316\u4e3a pdbqt \u6587\u4ef6\u3002<\/p>\n\n\n\n


2.1 \u51c6\u5907\u53d7\u4f53\u7684 pdbqt \u6587\u4ef6
2.1.1 \u4f7f\u7528 PyMol \u8f6f\u4ef6\u8fdb\u884c\u5904\u7406<\/p>\n\n\n\n


pdb \u4e0b\u8f7d\u7684\u86cb\u767d\u9700\u8981\u5148\u4f7f\u7528 PyMol \u8f6f\u4ef6\u5220\u9664\u591a\u4f59\u7684\u79bb\u5b50\u3001\u6c34\u5206
\u5b50\uff0c\u540c\u6e90\u591a\u805a\u4f53\u86cb\u767d\u8fd8\u53ef\u4ee5\u53ea\u4fdd\u7559\u4e00\u6761\u94fe\u3002\u76f4\u63a5\u4ece pdb \u4e0b\u8f7d\u86cb\u767d\u53ef\u4ee5
\u4f7f\u7528 fetch [protein name]\u547d\u4ee4\u3002\u5bfc\u5165\u540e pdb \u6587\u4ef6\u540e\uff0c\u70b9\u51fb\u53f3\u4e0b\u89d2\u7684 S
\u4ee5\u663e\u793a\u7ed3\u6784\u4fe1\u606f\u3001<\/p>\n\n\n\n

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

2.1.2 \u5173\u4e8e pdb \u6587\u4ef6\u7684\u683c\u5f0f<\/p>\n\n\n\n

\u8be5\u683c\u5f0f\u7701\u7565\u4e86\u4e00\u5207\u6c22\u539f\u5b50\uff0c\u5305\u62ec\u6e38\u79bb\u7684\u6c34\u5206\u5b50\u90fd\u53ea\u4fdd\u7559\u4e86\u4e00\u4e2a O\uff0c\u6240\u4ee5\u540e\u7eed\u9700\u8981\u52a0\u6c22\u64cd\u4f5c\u3002\u8be5\u6587\u4ef6\u7684\u683c\u5f0f\u8f83\u590d\u6742\uff0c\u6700\u597d\u4f7f\u7528\u6210\u719f\u7684\u8f6f\u4ef6\u8fdb\u884c\u7f16\u8f91\uff0c\u800c\u4e0d\u4e0a\u81ea\u884c\u7f16\u8f91\u3002\u8be5\u6587\u4ef6\u4e2d\u7684\u6c28\u57fa\u9178\u6b8b\u57fa\u7684\u539f\u5b50\u5168\u90e8\u8bb0\u5f55\u5728 ATOM \u884c\u4e2d\uff0c\u540e\u9762\u7684\u6bcf\u4e00\u9879\u5206\u522b\u4e3a\u539f\u5b50\u5e8f\u53f7\u3001\u539f\u5b50\u540d\u79f0\uff08\u7b2c\u4e00\u4e2a\u5b57\u6bcd\u4e3a\u539f\u5b50\u7684\u5143\u7d20\u7b26\u53f7\uff0c\u7b2c\u4e8c\u4e2a\u5b57\u6bcd\u4e3a\u8fdc\u8fd1\u6807\u8bc6\u7b26 A\u3001B\u3001G\u3001D\u3001E\u3001Z\u3001H \u5206\u522b\u5bf9\u5e94\u6709\u673a\u5316\u5408\u7269\u547d\u540d\u7cfb\u7edf\u4e2d\u7684 \u03b1\u3001\u03b2\u3001\u03b3\u3001\u03b4\u3001\u03b5\u3001\u03b6\u3001\u03b7\uff09\u3001\u6b8b\u57fa\u540d\u79f0\u3001\u94fe\u7f16\u53f7\u3001\u6b8b\u57fa\u5e8f\u53f7\u3001\u539f\u5b50\u5750\u6807\u7b49<\/p>\n\n\n\n

\u800c\u79bb\u5b50\u3001\u6c34\u5206\u5b50\u4ee5\u53ca\u7ed3\u5408\u5728\u86cb\u767d\u4e2d\u7684\u914d\u4f53\uff08\u5982\u6291\u5236\u5242\u7b49\uff09\u7b49\u975e\u86cb\u767d\u8d28\u7684\u90e8\u5206\u8bb0\u5f55\u5728 HETNAM\uff08\u975e\u6807\u51c6\u6b8b\u57fa\u7684\u540d\u79f0\uff09\u4e2d\uff1a<\/p>\n\n\n\n

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

\u540c\u6837\u7684\u4f9d\u6b21\u662f\u539f\u5b50\u7f16\u53f7\u3001\u539f\u5b50\u540d\u79f0\u3001\u57fa\u56e2\u540d\u79f0\uff08\u5982\u6c34\u8fd9\u91cc\u8d77\u540d\u4e3aHOH\uff09\u3001\u94fe\u7f16\u53f7\uff08\u4f46\u662f\u5b83\u672c\u8eab\u4e0d\u4f9d\u9644\u4e8e\u54ea\u6761\u94fe\uff09\u3001\u539f\u5b50\u7f16\u53f7\u3001\u5750\u6807\u7b49\u3002<\/p>\n\n\n\n

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

<\/p>\n\n\n\n

2.1.3 \u4f7f\u7528 PyMol \u547d\u4ee4\u8fdb\u884c\u9009\u62e9\u548c\u5220\u9664
\u9009\u62e9\u4e5f\u53ef\u4ee5\u4f7f\u7528\u547d\u4ee4\u9009\u62e9\uff0cselect \u547d\u4ee4\u53ef\u4ee5\u7528\u4e8e\u9009\u62e9\u94fe\u5982\uff1a
select chain A
indicate \u547d\u4ee4\u7684\u683c\u5f0f\u5219\u4e3a indicate [element_type] [name]\uff0c\u5982\u6839\u636e\u6b8b\u57fa
\u540d\u79f0 HOH \u9009\u62e9\u6240\u6709\u7684\u6c34\u5206\u5b50\uff1a
indicate resname HOH
\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u9009\u62e9\u6c34\u5206\u5b50\u4e0d\u8981\u4f7f\u7528\uff1a
indicate name O
\u5426\u5219\u5176\u4f1a\u9009\u4e2d\u6240\u6709\u6c28\u57fa\u9178\u6b8b\u57fa\u4e2d\u7684\u6c27\u539f\u5b50\u3002\u6839\u636e\u6b8b\u57fa\u540d\u79f0\u9009\u62e9\u914d\u4f53
Mr-Greyfun
\uff08\u793a\u4f8b\u4e2d\u914d\u4f53\u540d\u79f0\u4e3a STI\uff09\uff1a
indicate resname STI
\u6839\u636e\u539f\u5b50\u540d\u79f0\u9009\u62e9\u6c2f\u539f\u5b50\uff1a
indicate name CL
\u53ef\u4ee5\u4f7f\u7528 remove \u547d\u4ee4\u8fdb\u884c\u5220\u9664\u64cd\u4f5c\uff0c\u547d\u4ee4\u683c\u5f0f\u4e0e\u4e4b\u7c7b\u4f3c\uff1a
remove resname HOH
remove name CL
remove chain B<\/p>\n\n\n\n

2.1.1 \u4fdd\u5b58
\u5728 PyMol \u4e2d\u5b8c\u6210\u4e0a\u8ff0\u5904\u7406\u540e\u4f7f\u7528 Export Molecule-save \u4fdd\u5b58\u6210pdb \u683c\u5f0f\u7684\u6587\u4ef6\u3002
2.1.2 \u52a0\u6c22\u64cd\u4f5c
pdb \u6587\u4ef6\u4f1a\u7701\u7565\u6c22\u539f\u5b50\uff0c\u6240\u4ee5\u9700\u8981\u8fdb\u884c\u52a0\u6c22\uff0c\u53ef\u4ee5\u5728 PyMol \u4e2d\u4f7f\u7528 h_add \u547d \u4ee4 \u52a0\u6c22 \uff08\u5220\u9664\u4e3a remove hydrogen \uff09\uff0c \u4f46\u6700 \u597d \u4f7f \u7528AutoDockTools\uff08ADT\uff09\u8fdb\u884c\u52a0\u6c22\u3002\u5904\u7406\u597d\u540e\u7684\u6587\u4ef6\u7528 ADT \u6253\u5f00\u540e\uff0c\u70b9\u51fb Edit-Hydrogens-Add-OK\u3002\u52a0\u6c22\u3002
2.1.3 \u8f6c\u5316\u4e3a pdbqt \u683c\u5f0f\u7684\u6587\u4ef6
\u70b9\u51fb Grid-Macromolecule-Choose\uff0c\u9009\u62e9\u597d\u540e\u70b9 select molecule\uff0c
\u5b83\u4f1a\u81ea\u52a8\u52a0\u7535\u8377\u7b49\uff0c\u70b9 OK \u5373\u53ef\uff0c\u5b8c\u6210\u540e\uff0c\u4f1a\u5f39\u51fa\u4fdd\u5b58\u7a97\u53e3\uff0c\u76f4\u63a5\u4fdd
\u5b58 pdbqt \u683c\u5f0f\u5373\u53ef<\/p>\n\n\n\n

2.1.1 \u4fdd\u5b58
\u5728 PyMol \u4e2d\u5b8c\u6210\u4e0a\u8ff0\u5904\u7406\u540e\u4f7f\u7528 Export Molecule-save \u4fdd\u5b58\u6210
pdb \u683c\u5f0f\u7684\u6587\u4ef6\u3002
2.1.2 \u52a0\u6c22\u64cd\u4f5c
pdb \u6587\u4ef6\u4f1a\u7701\u7565\u6c22\u539f\u5b50\uff0c\u6240\u4ee5\u9700\u8981\u8fdb\u884c\u52a0\u6c22\uff0c\u53ef\u4ee5\u5728 PyMol \u4e2d\u4f7f
\u7528 h_add \u547d \u4ee4 \u52a0\u6c22 \uff08\u5220\u9664\u4e3a remove hydrogen \uff09\uff0c \u4f46\u6700 \u597d \u4f7f \u7528
AutoDockTools\uff08ADT\uff09\u8fdb\u884c\u52a0\u6c22\u3002
\u5904\u7406\u597d\u540e\u7684\u6587\u4ef6\u7528 ADT \u6253\u5f00\u540e\uff0c\u70b9\u51fb Edit-Hydrogens-Add-OK\u3002
\u52a0\u6c22\u3002
2.1.3 \u8f6c\u5316\u4e3a pdbqt \u683c\u5f0f\u7684\u6587\u4ef6
\u70b9\u51fb Grid-Macromolecule-Choose\uff0c\u9009\u62e9\u597d\u540e\u70b9 select molecule\uff0c
\u5b83\u4f1a\u81ea\u52a8\u52a0\u7535\u8377\u7b49\uff0c\u70b9 OK \u5373\u53ef\uff0c\u5b8c\u6210\u540e\uff0c\u4f1a\u5f39\u51fa\u4fdd\u5b58\u7a97\u53e3\uff0c\u76f4\u63a5\u4fdd
\u5b58 pdbqt \u683c\u5f0f\u5373\u53ef<\/p>\n\n\n\n

<\/p>\n\n\n\n

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

\u8bbe\u7f6e\u597d\u540e\u70b9 Done\uff0c\u7136\u540e\u70b9\u51fb Ligand-Output-Save as PDBQT \u5373\u53ef
\u4fdd\u5b58\u3002<\/p>\n\n\n\n

2.2.1 \u9644\uff1a\u7528 PyMol \u5bfc\u51fa pdb \u6587\u4ef6\u4e2d\u7684\u914d\u4f53\u7684\u65b9\u6cd5
\u5728\u754c\u9762\u4e0a\u9009\u4e2d\u5c0f\u5206\u5b50\uff0c\u70b9\u51fb(sele)\u7684 A-copy to object-new\u3002\u7ea2\u6846\u5185
\u7684\u533a\u57df\u53ef\u4ee5\u70b9\u51fb\u540e\u5c06\u5176\u5bf9\u5e94\u7684\u5bf9\u8c61\u9690\u85cf\u8d77\u6765\uff1a
\u7136\u540e\u70b9\u51fb Export Molecule-save \u4fdd\u5b58\u6210 pdb \u683c\u5f0f\u7684\u6587\u4ef6\u3002\u6ce8\u610f\uff0c\u8fd9\u4e2a
\u5185\u7f6e\u7684\u914d\u4f53\u4e5f\u662f\u6ca1\u6709\u52a0\u6c22\u7684\uff0c\u9700\u8981\u7528 ADT \u52a0\u6c22\u3002<\/p>\n\n\n\n

3 \u5bf9\u63a5
3.1 \u5bf9\u63a5\u64cd\u4f5c\u6b65\u9aa4
3.1.1 \u5bfc\u5165\u53d7\u4f53\u548c\u914d\u4f53
\u5728 ADT \u91cc\u9762\uff0c\u70b9\u51fb Grid-Macromolecule-Open \u6253\u5f00\u53d7\u4f53\u86cb\u767d
\u70b9\u51fb Grid-Set-Map-Types-Open Ligand \u6253\u5f00\u53d7\u4f53\u7684 pdbqt \u6587\u4ef6
3.1.2 \u5b9a\u4e49\u5bf9\u63a5\u76d2\u5b50
\u70b9\u51fb Grid-Grid Box \u5b9a\u4e49\u5bf9\u63a5\u76d2\u5b50
3.1.3 \u751f\u6210 config.txt \u6587\u4ef6
\u70b9\u51fb Docking-Output-Vina config \u751f\u6210 config.txt \u6587\u4ef6
3.1.4 \u542f\u52a8\u5bf9\u63a5<\/p>\n\n\n\n

\u89c6\u9891\u4e2d\u7684\u6b65\u9aa4\uff1a<\/p>\n\n\n\n

1\u3001\u5bfc\u5165protein\u86cb\u767d\u8d28<\/p>\n\n\n\n

2\u3001\u5220\u9664\u6c34\u5206\u5b50 \u5982\u679c\u4f60\u7684\u5bf9\u63a5\u533a\u57df\u6709\u6c34\u5206\u5b50\uff0c\u4f1a\u5f71\u54cd\u5bf9\u63a5\u7ed3\u679c<\/p>\n\n\n\n

pdq\u8be5\u683c\u5f0f\u7701\u7565\u4e86\u4e00\u5207\u6c22\u539f\u5b50\uff0c\u5305\u62ec\u6e38\u79bb\u7684\u6c34\u5206\u5b50\u90fd\u53ea\u4fdd\u7559\u4e86\u4e00\u4e2a O\uff0c\u6240\u4ee5\u540e\u7eed\u9700\u8981\u52a0\u6c22\u64cd\u4f5c\u3002 <\/p>\n\n\n\n

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

3\u3001edit ->hydrogens->add->polar only \u6b64\u65f6\u7ed3\u6784\u4e2d\u53d1\u4eae\u7684\u5c31\u662f\u6c22\u952e\uff08\u52a0\u6c22\uff09<\/p>\n\n\n\n

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

4\u3001\u52a0\u7535\u8377 edit -> charges->add kollman charges<\/p>\n\n\n\n

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

5 \u62a5\u5b58 grid -> macromolecule ->choose->select<\/p>\n\n\n\n

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

\u51c6\u5907\u914d\u4f53\u6587\u4ef6\uff1a<\/p>\n\n\n\n

\u4ee5sdf\u7ed3\u5c3e\u7684\u6587\u4ef6\u76f4\u63a5\u62d6\u8fdb AUTO\u8f6f\u4ef6\u4e2d\u4f1a\u62a5\u9519\uff0c\u9700\u8981\u8f6c\u6362\u6210pdb\u6587\u4ef6<\/p>\n\n\n\n

\u53ef\u4ee5\u4f7f\u7528pymol\u53ef\u89c6\u5316\u5de5\u5177\u8f6c\u6362(\u6ce8\u610f\uff1a\u914d\u4f53 \u82f1\u6587 ligend)<\/p>\n\n\n\n

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

1\u3001\u5c06\u8be5\u6587\u4ef6\u62d6\u52a8\u5230pymol\u4e2d\u6253\u5f00\uff0cfile ->molecule<\/p>\n\n\n\n

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

\u914d\u4f53\u6587\u4ef6\uff1a<\/p>\n\n\n\n

1\u3001\u6253\u5f00auto dock\uff0c\u5c06\u914d\u4f53\u6587\u4ef6\u5bfc\u5165\uff1a<\/p>\n\n\n\n

2\u3001 \u70b9\u51fb Ligand\uff08\u914d\u4f53\uff09->input->choose (\u8fd9\u4e00\u6b65\u5c31\u662f\u751f\u6210\u4e86\u914d\u4f53\u6587\u4ef6)<\/p>\n\n\n\n

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

3\u3001\u70b9\u51fb Ligand\uff08\u914d\u4f53\uff09->output->save as pdbqt<\/p>\n\n\n\n

\u63a5\u4e0b\u6765\u5c31\u53ef\u4ee5\u8fdb\u884c\u5206\u5b50\u5bf9\u63a5\uff1a<\/p>\n\n\n\n

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

1\u3001\u5c06\u4e24\u4e2a\uff08\u53d7\u4f53\u548c\u914d\u4f53\uff09pdpqt\u5bfc\u5165<\/p>\n\n\n\n

2\u3001\u91cd\u65b0\u9009\u62e9\u86cb\u767d\u8d28\u5206\u5b50\u4f5c\u4e3a\u53d7\u4f53<\/p>\n\n\n\n

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

\u70b9\u51fbNO<\/p>\n\n\n\n

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

\u63a5\u4e0b\u6765\u8bbe\u7f6e\u5bf9\u63a5\u76d2\u5b50\uff1a<\/p>\n\n\n\n

grid -> grid box<\/p>\n\n\n\n

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

\u8bbe\u7f6e\u76d2\u5b50\u4f4d\u7f6e\uff08spacing\u8bbe\u7f6e\u4e3a1\uff09<\/p>\n\n\n\n

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

\u7136\u540e grid box \u5f39\u51fa\u8bbe\u7f6e\u4e2d\u9009\u62e9 file->output grid dimensions file\uff08\u4fdd\u5b58\u76d2\u5b50\u8bbe\u7f6e\uff09<\/p>\n\n\n\n

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

\u4fdd\u5b58\uff1a<\/p>\n\n\n\n

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

\u65b0\u5efaconfig.txt:\u7528\u4e8e\u542f\u52a8vina<\/p>\n\n\n\n

receptor \u86cb\u767d\u8d28\u540d\uff08\u751f\u6210\u7684\u86cb\u767d\u8d28\u6587\u4ef6\u540d\uff09<\/p>\n\n\n\n

ligand \u914d\u4f53\u540d<\/p>\n\n\n\n

center \u548csize\u5728\u4e0a\u4e00\u6b65\u7684grid\u4e2d\u6709<\/p>\n\n\n\n

receptor\uff1a\u6307\u5b9a\u53d7\u4f53\u5206\u5b50\u7684\u8def\u5f84<\/p>\n\n\n\n

ligand\uff1a\u914d\u4f53\u5206\u5b50\u7684\u8def\u5f84<\/p>\n\n\n\n

center_x\uff0ccenter_y\uff0ccenter_z\uff1a\u641c\u7d22\u7a7a\u95f4\u4e2d\u5fc3\u7684\u5750\u6807<\/p>\n\n\n\n

size_x\uff0csize_y\uff0csize_z\uff1a\u6307\u5b9a\u641c\u7d22\u7a7a\u95f4\u7684\u5927\u5c0f\u3002\u8fd9\u91cc\u8bbe\u7f6e\u7684\u5927\u5c0f\u57fa\u672c\u5c31\u662f\u628a\u6574\u4e2a\u53d7\u4f53\u5206\u5b50\u90fd\u5305\u542b\u4e86\uff0c\u5c5e\u4e8eblind docking\u3002\u5982\u4f55\u66f4\u51c6\u786e\u786e\u5b9a\u7ed3\u5408\u53e3\u888b\u7684\u4f4d\u7f6e\uff0c\u6211\u4eec\u7a0d\u540e\u518d\u8bf4\u3002<\/p>\n\n\n\n

energy_range\uff1a\u9ed8\u8ba44\uff0c\u4e0e\u6700\u4f18\u7ed3\u5408\u6a21\u578b\u76f8\u5dee\u7684\u6700\u5927\u80fd\u91cf\u503c\uff0c\u5355\u4f4d\u662fkcal\/mol\u3002\u6bd4\u65b9\u8bf4\uff0c\u6700\u4f18\u6a21\u578b\u7684\u80fd\u91cf\u8ba1\u7b97\u51fa\u6765\u662f-8.5kcal\/mol\uff0c\u90a3\u4e48vina\u4e5f\u5c31\u6700\u591a\u8ba1\u7b97\u5230-4.5kcal\/mol\u7684\u6a21\u578b\u5c31\u7ec8\u6b62\u4e86\uff0c\u4e5f\u5c31\u610f\u5473\u7740\u8fd9\u4e2a\u503c\u51b3\u5b9a\u4e86\u751f\u6210\u6a21\u578b\u7684\u6700\u5927\u4e2a\u6570\u3002<\/p>\n\n\n\n

exhaustiveness\uff1a\u7528\u6765\u63a7\u5236\u5bf9\u63a5\u7684\u7ec6\u81f4\u7a0b\u5ea6\uff0c\u9ed8\u8ba4\u503c\u662f8. \u5927\u81f4\u4e0e\u65f6\u95f4\u6210\u6b63\u6bd4\u3002<\/p>\n\n\n\n

num_modes\uff1a\u6700\u591a\u751f\u6210\u591a\u5c11\u4e2a\u6a21\u578b\u3002\u5b9e\u9645\u751f\u6210\u7684\u6a21\u578b\u6570\u7531num_modes\u548cenergy_range\u5171\u540c\u51b3\u5b9a\u3002<\/p>\n\n\n\n

energy_range<\/pre>\n\n\n\n
 maximum energy difference between the best binding \n mode and the worst one displayed (kcal\/mol)<\/pre>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u6700\u540e\u542f\u52a8vina \u8fdb\u884c\u5206\u5b50\u5bf9\u63a5:<\/p>\n\n\n\n
\u5728config\u76ee\u5f55\u4e2d\u6253\u5f00cmd->\u8f93\u5165vina<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u5176\u4e2d\uff1a\u8fd9\u6761\u547d\u4ee4\u5c31\u662f\u5229\u7528config.txt\u6587\u4ef6\u8fdb\u884c\u5206\u5b50\u5bf9\u63a5(cmd \u5fc5\u987b\u5728config\u6587\u4ef6\u76ee\u5f55\u4e0b\u6253\u5f00)<\/p>\n\n\n\n
<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u6267\u884c \u547d\u4ee4\uff1a<\/p>\n\n\n\n
D:\\Autodock\\pdbqt>”D:\\Vina\\vina.exe” –receptor protein.pdbqt –ligand ligend.pdbqt –config config.txt –log log.txt –out output.pdbqt<\/p>\n\n\n\n
<\/p>\n\n\n\n
“D:\\Vina\\vina.exe” –receptor selected_prediction_ready.pdbqt –ligand Conformer3D_CID_65536.pdbqt –config config.txt –log log.txt –out output.pdbqt<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u5982\u679c\u4e0a\u8ff0\u547d\u4ee4\u62a5\u9519\uff0c\u4e00\u822c\u662f\u751f\u6210\u7684config\u6587\u4ef6\u6709\u95ee\u9898\uff1a<\/p>\n\n\n\n
\u6b63\u786e\u7684config\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u6267\u884c\u5b8c\u6bd5\u53ef\u4ee5\u770b\u5230\u751f\u6210\u4e00\u4e2alog\u6587\u4ef6<\/p>\n\n\n\n
vina \u4e2d\u7684affinity\u662f\u4eb2\u5408\u529b\u7ed3\u679c\u6392\u540d<\/p>\n\n\n\n
\u6700\u540e\uff1a<\/p>\n\n\n\n
\u67e5\u770b\u751f\u6210\u7684\u6a21\u578b\uff1a<\/p>\n\n\n\n
\u5c06protein\u548coutput\u8f93\u51fa\u5bfc\u5165pymol<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\u70b9\u51fb  all -> s\u67e5\u770b\u8868\u9762 \u7ed3\u6784<\/p>\n\n\n\n
\u70b9\u51fb\u5de6\u53f3\u7bad\u5934\u67e5\u770b\u4e0d\u540c\u7684\u7ed3\u6784\uff1a<\/p>\n\n\n\n
\"\"<\/figure>\n\n\n\n
5.\u6211\u4eec\u6311\u9009\u7b2c\u4e00\u4e2a\u6a21\u578b\uff0c\u770b\u770b\u7ed3\u6784\u65b9\u5f0f\u662f\u600e\u6837\u7684\uff0c\u89c1\u4e0b\u56fe\u3002\u5f88\u663e\u7136\u4e0e\u771f\u5b9e\u7684\u7ed3\u5408\u65b9\u5f0f\u76f8\u5dee\u751a\u8fdc\uff0c\u53ef\u4ee5\u8bf4\u662f\u5b8c\u5168\u9519\u8bef\u3002<\/p>\n\n\n\n
\"-1.jpg\"<\/figure>\n\n\n\n
\u4e3a\u4ec0\u4e48\u4f1a\u51fa\u73b0\u8fd9\u79cd\u60c5\u51b5\uff0c\u5f88\u5927\u7a0b\u5ea6\u4e0a\u662f\u56e0\u4e3asearch space\u592a\u5927\uff0c\u53ef\u80fd\u9700\u8981\u8bbe\u7f6e\u66f4\u5927\u7684exhaustiveness\u3002<\/p>\n\n\n\n
\u5982\u679c\u6211\u4eec\u5927\u81f4\u77e5\u9053binding pocket\u5728\u4ec0\u4e48\u4f4d\u7f6e\uff0c\u90a3\u51c6\u786e\u6027\u5e94\u8be5\u4f1a\u9ad8\u4e0d\u5c11\uff0c\u5982\u4f55\u5927\u81f4\u786e\u5b9abinding pocket\u7684\u4f4d\u7f6e\u5462\uff1f\u6211\u4eec\u63a5\u7740\u8bd5\u9a8c\u3002<\/p>\n\n\n\n
\u53ef\u4ee5\u901a\u8fc7\u5b9e\u9a8c\u7684\u65b9\u5f0f\uff0c\u6bd4\u5982\u67d0\u4e2a\u70b9\u7a81\u53d8\u5bf9\u7ed3\u5408\u6216\u8005\u6d3b\u6027\u5f71\u54cd\u975e\u5e38\u5927\uff0c\u90a3\u4e48\u5927\u6982\u7387\u8fd9\u4e2a\u6b8b\u57fa\u662f\u7ed3\u5408\u53e3\u888b\u7684\u4e00\u90e8\u5206\u3002<\/p>\n\n\n\n
\u53ef\u4ee5\u901a\u8fc7\u8f6f\u4ef6\u9884\u6d4b\uff0c\u6bd4\u5982\u86cb\u767d\u4e0e\u914d\u4f53\uff08\u5e95\u7269\uff09\u7ed3\u5408\u4f4d\u70b9\u9884\u6d4b\uff1ahttps:\/\/zhanglab.ccmb.med.umich.edu\/COACH\/<\/a><\/p>\n\n\n\n
\u518d\u6bd4\u5982Discovery studio\u8f6f\u4ef6\uff08\u4e13\u4e1a\u7248\u7684\uff09\uff0c\u53ef\u4ee5\u5f88\u65b9\u4fbf\u7684\u6839\u636e\u53d7\u4f53\u5206\u5b50\u7684\u8868\u9762\u5f62\u72b6\u6765\u9884\u6d4b\u7ed3\u5408\u53e3\u888b\u4f4d\u7f6e\u3002<\/p>\n\n\n\n
\"20190507175152.png\"<\/figure>\n\n\n\n
\u53e3\u888b\u7684\u5750\u6807\u4e3a\uff1a<\/p>\n\n\n\n
34.3356\uff0c14.9412\uff0c26.9615<\/p>\n\n\n\n
\u6211\u4eec\u4fee\u6539\u4e0b\u5bf9\u63a5\u53c2\u6570\uff0c\u65b0\u7684\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n\n\n\n
receptor = r.pdbqt<\/p>\n\n\n\n
ligand = nap.pdbqt<\/p>\n\n\n\n
center_x = 34.3356<\/p>\n\n\n\n
center_y = 14.9412<\/p>\n\n\n\n
center_z = 26.9615<\/p>\n\n\n\n
size_x = 30.0<\/p>\n\n\n\n
size_y = 30.0<\/p>\n\n\n\n
size_z = 30.0<\/p>\n\n\n\n
energy_range = 4<\/p>\n\n\n\n
exhaustiveness = 10<\/p>\n\n\n\n
num_modes = 10<\/p>\n\n\n\n
\u6700\u4f18\u7ed3\u679c\u4e0e\u771f\u5b9e\u6a21\u578b\u7684RMSD\u4e3a1.795\u57c3\uff0c\u53ef\u4ee5\u8bf4\u975e\u5e38\u7cbe\u51c6\u4e86<\/p>\n\n\n\n
\u6bd4\u5bf9\u7ed3\u679c\u5982\u4e0b\uff1a<\/p>\n\n\n\n
\"\"\/<\/figure>\n\n\n\n
Souce: \u7ebd\u666e\u751f\u7269<\/a>    2019-05-07<\/p>\n\n\n\n
<\/p>\n\n\n\n
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fetch 5ocn#foxn1\nfetch 3uf0#\nfetch 1si4#\u8840\u7ea2\u86cb\u767d<\/code><\/pre>\n\n\n\n
\u53bb\u9664\u6c34\u5206\u5b50<\/h2>\n\n\n\n
remove solvent\n<\/code><\/pre>\n\n\n\n
\u5206\u79bb\u5f97\u5230\u86cb\u767d<\/h2>\n\n\n\n
remove organic<\/code><\/pre>\n\n\n\n
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http:\/\/pymol.chenzhaoqiang.com\/intro\/startManual.html<\/a><\/p>\n\n\n\n
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<\/p>\n","protected":false},"excerpt":{"rendered":"
\u4efb\u52a1\uff1a 1\u3001\u5b89\u88c5\u5b66\u4e60yutobe\u4e0a\u9762\u7684\u8f6f\u4ef6 https:\/\/www.youtube.com\/watch?v=S … \u7ee7\u7eed\u9605\u8bfbAI\u5236\u836f \uff1a \u5206\u5b50\u5bf9\u63a5<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[4,16],"tags":[],"_links":{"self":[{"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/posts\/2712"}],"collection":[{"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/comments?post=2712"}],"version-history":[{"count":82,"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/posts\/2712\/revisions"}],"predecessor-version":[{"id":3625,"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/posts\/2712\/revisions\/3625"}],"wp:attachment":[{"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/media?parent=2712"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/categories?post=2712"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/139.9.1.231\/index.php\/wp-json\/wp\/v2\/tags?post=2712"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}