{"id":5012,"date":"2022-07-24T09:34:11","date_gmt":"2022-07-24T01:34:11","guid":{"rendered":"http:\/\/139.9.1.231\/?p=5012"},"modified":"2022-07-24T09:34:13","modified_gmt":"2022-07-24T01:34:13","slug":"abacus-r","status":"publish","type":"post","link":"http:\/\/139.9.1.231\/index.php\/2022\/07\/24\/abacus-r\/","title":{"rendered":"\u5229\u7528\u6df1\u5ea6\u5b66\u4e60\u8fed\u4ee3\u81ea\u6d3d\u7684\u86cb\u767d\u5e8f\u5217\u8bbe\u8ba1"},"content":{"rendered":"\n

\u2014\u2014\u80cc\u666f\u2014\u2014<\/strong><\/p>\n\n\n\n

\u73b0\u6709\u7684\u57fa\u4e8e\u86cb\u767d\u7ed3\u6784\u7684\u6df1\u5ea6\u5b66\u4e60\u5e8f\u5217\u8bbe\u8ba1\u65b9\u6cd5\uff0c\u867d\u7136\u5728\u6d4b\u8bd5\u7684\u8ba1\u7b97\u6307\u6807\u4e0a\u53d6\u5f97\u4e86\u5f88\u597d\u7684\u6210\u679c\uff0c\u4f46\u662f\u8fd8\u9c9c\u6709\u65b9\u6cd5\u7ecf\u8fc7\u5b9e\u9a8c\u7684\u8003\u9a8c\u4ecd\u7136\u8d85\u8d8a\u4f20\u7edf\u7684\u80fd\u91cf\u51fd\u6570\u65b9\u6cd5\u3002\u57fa\u4e8e\u8fd9\u4e00\u6311\u6218\uff0c\u4e2d\u56fd\u79d1\u5b66\u6280\u672f\u5927\u5b66\u7684\u5218\u6d77\u71d5\u6559\u6388\u8bfe\u9898\u7ec4\uff0c\u53d1\u5c55\u4e86\u540d\u4e3aABACUS-R\u65b9\u6cd5\uff0c\u76f8\u5173\u5de5\u4f5c\u540d\u4e3aRotamer-free protein sequence design based on deep learning and self-consistency\uff0c\u4e8e\u8fd1\u671f\u53d1\u8868\u5728Nature Computational Science<\/em>\u4e0a\u3002<\/p>\n\n\n\n

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

\u56fe1. ABACUS-R\u65b9\u6cd5\u7684\u793a\u610f\u56fe<\/p>\n\n\n\n

<\/strong> \u2014\u2014\u65b9\u6cd5\u2014\u2014<\/strong><\/p>\n\n\n\n

ABACUS-R\u65b9\u6cd5\u5305\u542b\u4e24\u90e8\u5206\uff1a\uff081\uff09\u4e00\u4e2aencoder-decoder\u7f51\u7edc\u88ab\u9884\u8bad\u7ec3\u7528\u4ee5\u63a8\u65ad\u7ed9\u5b9a\u9aa8\u67b6\u7684\u5c40\u90e8\u73af\u5883\u65f6\u4e2d\u5fc3\u6b8b\u57fa\u7684\u4fa7\u94fe\u7c7b\u578b\u00a0\uff082\uff09\u7528\u8be5encoder-decoder\u7f51\u7edc\u8fde\u7eed\u66f4\u65b0\u6bcf\u4e2a\u6b8b\u57fa\u7684\u7c7b\u578b\uff0c\u6700\u7ec8\u6536\u655b\u83b7\u5f97\u81ea\u6d3d\uff08self-consistent\uff09\u3002\u7f51\u7edc\u7684\u8f93\u5165\u662f\u4e2d\u5fc3\u6b8b\u57fa\u4e0e\u7a7a\u95f4\u4e0a\u6700\u90bb\u8fd1\uff08C\u03b1<\/sub>\u95f4\u8ddd\u79bb\uff09k\u4e2a\u6b8b\u57fa\u7ec4\u6210\u7684\u5c40\u90e8\u7ed3\u6784\u3002\u90bb\u8fd1\u6b8b\u57fa\u7684\u7279\u5f81\u5305\u542b\u7a7a\u95f4\u5c42\u9762\u7684\u76f8\u5bf9\u4f4d\u7f6e\u4e0e\u53d6\u5411\u4fe1\u606f\uff08XSPA<\/sub>\uff09\u3001\u5e8f\u5217\u5c42\u9762\u7684\u76f8\u5bf9\u4f4d\u7f6e\u4fe1\u606f\uff08XRSP<\/sub>\uff09\u4ee5\u53ca\u90bb\u8fd1\u6b8b\u57fa\u7684\u6b8b\u57fa\u7c7b\u578b\uff08XAA<\/sub>\uff09\u3002\u7b2ci\u4e2a\u4e2d\u5fc3\u6b8b\u57fa\u7684\u7279\u5f81\u5305\u542b\u5168\u96f6\u7684XSPA<\/sub>\u3001\u88abmask\u7684XAA<\/sub>\u4ee5\u53ca\u9aa8\u67b6\u4e0a\u768415\u4e2a\u03d5i<\/sub><\/em>\u22122<\/sub>,\u00a0\u03c8i<\/sub><\/em>\u22122<\/sub>,\u00a0\u03c9i<\/sub><\/em>\u22122<\/sub>\u2009\u22ef\u2009\u03d5i<\/sub><\/em>+2<\/sub>,\u00a0\u03c8i<\/sub><\/em>+2<\/sub>,\u00a0\u03c9i<\/sub><\/em>+2<\/sub>\uff0c\u8fd9\u4e9b\u7279\u5f81\u7ec4\u5408\u8d77\u6765\u4f1a\u88ab\u6620\u5c04\u5230\u4e0e\u90bb\u8fd1\u6b8b\u57fa\u7279\u5f81\u76f8\u540c\u7684\u7ef4\u5ea6\u3002\u4ee5\u4e0a\u6a21\u578b\u8f93\u5165\u7684\u4fe1\u606f\u90fd\u662f\u65cb\u8f6c\u5e73\u79fb\u4e0d\u53d8\u7684\u3002\u5c40\u90e8\u7ed3\u6784\u4e2d\u7684\u6240\u6709\u6b8b\u57fa\u7684\u7279\u5f81\u7ecf\u8fc7\u53ef\u5b66\u4e60\u7684\u6620\u5c04\u540e\u878d\u5408\u540e\uff0c\u5f97\u5230\u6bcf\u4e2a\u6b8b\u57fa\u603b\u7279\u5f81En\u3002{E<\/strong>n<\/sub><\/em>;\u2009n<\/em>\u2009=\u20090,\u20091,\u20092,\u2009…\u2009,\u2009k<\/em>}\u7ecf\u8fc7\u57fa\u4e8etransformer\u67b6\u6784\u7684encoder-decoder\uff0c\u9884\u6d4b\u6bcf\u4e2a\u4e2d\u5fc3\u6b8b\u57fa\u7684\u7c7b\u578b\u4ee5\u53ca\u5176\u4ed6\u8f85\u52a9\u4efb\u52a1\u3002<\/p>\n\n\n\n

\u81ea\u6d3d\u8fed\u4ee3\u8bbe\u8ba1\u7684\u65b9\u6cd5\u662f\uff1a\u5bf9\u5e8f\u5217\u968f\u673a\u521d\u59cb\u5316\uff0c\u7b2c\u4e00\u8f6e\u968f\u673a\u9009\u62e980%\u7684\u6b8b\u57fa\u901a\u8fc7encoder-decoder\u5e76\u884c\u9884\u6d4b\u5176\u6b8b\u57fa\u7c7b\u578b\uff0c\u4ee5\u540e\u6bcf\u8f6e\u968f\u673a\u9009\u62e9\u7684\u6b8b\u57fa\u6570\u76ee\u9010\u6e10\u4e0b\u964d\u3002\u6700\u7ec8\u7684\u8bbe\u8ba1\u7ed3\u679c\u4f1a\u9010\u6e10\u6536\u655b\u3002<\/p>\n\n\n\n

\u4f5c\u8005\u5c06PDB\u4e2d\u7684\u975e\u5197\u4f59\u7ed3\u6784\u6309\u7167\u4e24\u79cd\u4e0d\u540c\u7684\u65b9\u5f0f\u5212\u5206\u4e8695%\u4f5c\u4e3a\u8bad\u7ec3\u96c6\u30015%\u4f5c\u4e3a\u6d4b\u8bd5\u96c6\uff0c\u7b2c\u4e00\u79cd\u5212\u5206\u65b9\u5f0f\u786e\u4fdd\u6d4b\u8bd5\u96c6\u7684\u7ed3\u6784\u4e0d\u4f1a\u5b58\u5728\u8bad\u7ec3\u96c6\u4e2d\u51fa\u73b0\u8fc7\u7684CATH\u62d3\u6251\uff0c\u8bad\u7ec3\u5f97\u5230\u7684\u6a21\u578b\u4e3aModel\u00ad\u00adeval<\/sub>;\u7b2c\u4e8c\u79cd\u5212\u5206\u65b9\u5f0f\u65f6\u968f\u673a\u5212\u5206Modelfinal<\/sub>\u3002Model\u00ad\u00adeval<\/sub>\u53ef\u4ee5\u7528\u6765\u8bc4\u4f30\u6a21\u578b\u80fd\u529b\u7684\u65e0\u504f\u5411\u6027\u7684\u8868\u73b0\uff0c\u800cModelfinal<\/sub>\u4f7f\u7528\u4e86\u66f4\u4e30\u5bcc\u7684\u6570\u636e\u8bad\u7ec3\u8868\u73b0\u5e94\u5f53\u66f4\u597d\u3002<\/p>\n\n\n\n

<\/strong> \u2014\u2014\u8868\u73b0\u8bc4\u4f30\u2014\u2014<\/strong><\/p>\n\n\n\n

Encoder-decoder\u7684\u67b6\u6784\u53ef\u4ee5\u8fdb\u884c\u591a\u4efb\u52a1\u5b66\u4e60\uff0c\u9664\u4e86\u8bad\u7ec3\u5e8f\u5217\u7684\u6062\u590d\u7684\u4efb\u52a1\u4ee5\u5916\uff0c\u8fd8\u53ef\u4ee5\u9884\u6d4b\u4e8c\u7ea7\u7ed3\u6784\u3001SASA\u3001B-factor\u4e0e\u4fa7\u94fe\u626d\u8f6c\u89d2\u03c71<\/sub>\u3001\u03c72<\/sub>\u3002\u591a\u4e2a\u4efb\u52a1\u53ef\u4ee5\u589e\u5f3a\u6a21\u578b\u8bbe\u8ba1\u5e8f\u5217\u7684\u80fd\u529b\uff08\u56fe2a\uff09\uff0cModel\u00ad\u00adeval<\/sub>\u4e0eModel\u00ad\u00adfinal<\/sub>\u90fd\u53ef\u4ee5\u5728\u6d4b\u8bd5\u96c6\u4e0a\u6700\u597d\u53d6\u5f9750%\u5de6\u53f3\u51c6\u786e\u5ea6\u3002\u5728\u6d4b\u8bd5\u96c6\u4e0a\u7684\u7ed3\u679c\u663e\u793a\uff0c\u867d\u7136\u6709\u4e9b\u6b8b\u57fa\u7c7b\u578b\u6ca1\u6709\u6062\u590d\u6b63\u786e\uff0c\u4f46\u662f\u6a21\u578b\u4e5f\u5b66\u4e60\u5230\u4e86\u66ff\u6362\u4e3a\u6027\u8d28\u76f8\u4f3c\u7684\u6b8b\u57fa\uff08\u56fe2b\uff09\u3002<\/p>\n\n\n\n

\"\"
\u56fe2.\u00a0Model\u00ad\u00adeval<\/sub>\u5728\u4e0d\u540c\u4efb\u52a1\u7c7b\u578b\u4e0b\u7684\u8868\u73b0<\/figcaption><\/figure>\n\n\n\n

Decoder\u7f51\u7edc\u8f93\u51fa\u7684\u662f\u6bcf\u4e2a\u4f4d\u7f6e\u4e0a\u6b8b\u57fa\u7c7b\u578b\u7684-logP\uff0c\u7c7b\u4f3c\u4e8e\u9009\u62e9\u4e0d\u540c\u6b8b\u57fa\u5bf9\u5e94\u7684\u80fd\u91cf\uff0c\u6240\u4ee5\u4f5c\u8005\u5c06ProTherm\u6570\u636e\u96c6\u4e2d\u86cb\u767d\u7a81\u53d8\u7684\u0394\u0394G<\/em>\u4e0e\u6a21\u578b\u8ba1\u7b97\u51fa\u76f8\u5e94\u7684\u2212\u0394\u0394logits\u8fdb\u884c\u4e86\u6bd4\u8f83\uff0c\u53d1\u73b0\u4e8c\u8005\u6709\u4e00\u5b9a\u7684\u76f8\u5173\u6027\uff08\u56fe2d\uff09\uff0c\u8bf4\u660e\u6a21\u578b\u4e00\u5b9a\u7a0b\u5ea6\u4e0a\u5b66\u4e60\u5230\u4e86\u80fd\u91cf\u3002<\/p>\n\n\n\n

\u63a5\u7740\uff0c\u4f5c\u8005\u9a8c\u8bc1\u4e86\u6a21\u578b\u7684\u81ea\u6d3d\u6027\uff0c\u6d4b\u8bd5\u96c6\u4e2d100\u4e2a\u86cb\u767d\u5c5e\u4e8eCATH\u7684\u4e09\u4e2a\u5927\u7c7b\uff0c\u5bf9\u5176\u4e2d\u7684\u6bcf\u4e2a\u86cb\u767d\u4ece\u968f\u673a\u5e8f\u5217\u51fa\u53d1\u8bbe\u8ba110\u6761\u5e8f\u5217\uff0c\u968f\u7740\u8fed\u4ee3\u7684\u6b21\u6570\u53d8\u591a\uff0c\u5e73\u5747-logP\u4f1a\u8d8b\u4e8e\u6536\u655b\uff08\u56fe3a\uff09\uff0c\u540c\u65f6\u672a\u6536\u655b\u7684\u6b8b\u57fa\u6bd4\u4f8b\u4e5f\u4f1a\u6536\u655b\uff08\u56fe3b\uff09\u3002\u4e0d\u540cCATH\u7c7b\u522b\u7684\u9aa8\u67b6\u4e0a\u53d6\u5f97\u7684\u5e8f\u5217\u6062\u590d\u7387\u5dee\u8ddd\u4e0d\u5927\uff08\u56fe3c\uff09\u3002\u540c\u4e00\u86cb\u767d\u9aa8\u67b6\u8bbe\u8ba1\u51fa\u7684\u5e8f\u5217\u4f1a\u6709\u5f88\u9ad8\u7684\u76f8\u4f3c\u6027\uff080.76-0.89\uff09\u3002\u8bbe\u8ba1\u51fa\u7684\u5e8f\u5217\u4e0e\u5929\u7136\u5e8f\u5217\u76f8\u6bd4\uff0c\u5e8f\u5217\u7684\u6210\u5206\u9ad8\u5ea6\u76f8\u4f3c\uff08\u56fe3d\uff09\uff0cPearson\u76f8\u5173\u7cfb\u6570\u8fbe\u5230\u4e860.93\uff0c\u4f46GLU\u3001ALA\u4e0eLYS\u51fa\u73b0\u5f97\u66f4\u9891\u7e41\uff0c\u800cGln\u3001His\u3001Met\u51fa\u73b0\u5f97\u66f4\u5c11\u3002\u6b64\u5916\uff0cABACUS-R\u8bbe\u8ba1\u51fa\u7684\u5e8f\u5217\u4e0eABACUS\u8bbe\u8ba1\u51fa\u7684\u5e8f\u5217\u76f8\u6bd4\uff0c\u5e73\u5747\u6bcf\u4e2a\u6b8b\u57fa\u7684Rosetta\u6253\u5206\u66f4\u4f4e\uff08\u56fe3e\uff09\uff0c\u800c\u5e73\u5747\u7684-logP\u6253\u5206\u5374\u66f4\u9ad8\uff08\u56fe3f\uff09\uff0c\u8fd9\u610f\u5473\u7740ABACUS-R\u5b66\u4e60\u5230\u7684\u80fd\u91cf\u4e0eRosetta\u6253\u5206\u51fd\u6570\u5b58\u5728\u6b63\u4ea4\u7684\u90e8\u5206\u3002<\/p>\n\n\n\n

\"\"
\u56fe3.\u00a0ABACUS-R\u7684\u81ea\u6d3d\u80fd\u529b\u3001\u8bbe\u8ba1\u80fd\u529b\u4ee5\u53ca\u5b66\u4e60\u5230\u7684\u80fd\u91cf\u4e0eRosetta\u6253\u5206\u7684\u6bd4\u8f83<\/figcaption><\/figure>\n\n\n\n

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

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