{"id":44561,"date":"2023-08-18T16:43:45","date_gmt":"2023-08-18T08:43:45","guid":{"rendered":"https:\/\/swarma.org\/?p=44561"},"modified":"2023-08-18T16:43:45","modified_gmt":"2023-08-18T08:43:45","slug":"pnas-%e9%80%9f%e9%80%92%ef%bc%9a%e8%9b%8b%e7%99%bd%e8%b4%a8%e7%bb%93%e6%9e%84%e9%a2%84%e6%b5%8b%e4%b8%ad-transformer-%e7%9a%84%e5%8f%98%e6%8d%a2%e8%83%bd%e5%8a%9b","status":"publish","type":"post","link":"https:\/\/swarma.org\/?p=44561","title":{"rendered":"PNAS \u901f\u9012\uff1a\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\u4e2d transformer \u7684\u53d8\u6362\u80fd\u529b"},"content":{"rendered":"
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\u5173\u952e\u8bcd\uff1aTransformer\u795e\u7ecf\u7f51\u7edc\uff0c\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\uff0c\u7ed3\u6784\u751f\u7269\u5b66<\/span><\/strong><\/strong><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/span><\/strong><\/strong><\/strong><\/span><\/p>\n


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\u8bba\u6587\u9898\u76ee\uff1aThe transformative power of transformers in protein structure <\/span>prediction<\/span><\/section>\n

\u671f\u520a\u540d\u79f0\uff1aPNAS<\/em><\/span><\/p>\n

\u6591\u56fe\u5730\u5740\uff1ahttps:\/\/pattern.swarma.org\/paper\/4959892e-2ffe-11ee-a742-0242ac17000d<\/span><\/p>\n

\u8bba\u6587\u5730\u5740\uff1ahttps:\/\/www.pnas.org\/doi\/10.1073\/pnas.2303499120<\/span><\/p>\n

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Transformer\u795e\u7ecf\u7f51\u7edc\u4ee5\u524d\u6240\u672a\u6709\u7684\u9ad8\u51c6\u786e\u6027\u9884\u6d4b\u86cb\u767d\u8d28\u7ed3\u6784\uff0c\u5f7b\u5e95\u6539\u53d8\u4e86\u7ed3\u6784\u751f\u7269\u5b66\u3002\u8fd9\u65b9\u9762\u7684\u6807\u5fd7\u6027\u4e8b\u4ef6\u662f2020\u5e74\uff0cDeepMind\u7684AlphaFold2\u65b9\u6cd5\u5728\u4ece\u6c28\u57fa\u9178\u5e8f\u5217\u9884\u6d4b\u86cb\u767d\u8d28\u7684\u4e09\u7ef4\u7ed3\u6784\u65b9\u9762\u53d6\u5f97\u4e86\u91cd\u5927\u79d1\u5b66\u7a81\u7834\u3002AlphaFold2\u6846\u67b6\u7684\u6838\u5fc3\u662f\u7531\u6ce8\u610f\u529b\u673a\u5236\u9a71\u52a8\u7684Transformer\u795e\u7ecf\u7f51\u7edc\u7ec4\u6210\u3002Transformer\u67b6\u6784\u4e4b\u6240\u4ee5\u975e\u5e38\u5f3a\u5927\uff0c\u662f\u56e0\u4e3a\u5b83\u80fd\u591f\u6a21\u62df\u8f93\u5165\u5e8f\u5217\u4e2d\u8d85\u51fa\u5176\u987a\u5e8f\u90bb\u57df\u7684\u957f\u7a0b\u5173\u7cfb\u3002\u5728AlphaFold\u6210\u529f\u7684\u540c\u65f6\uff0cRoseTTAFold\u3001OmegaFold\u7b49\u6846\u67b6\u4e5f\u5728\u5feb\u901f\u53d1\u5c55\u3002\u81eaAlphaFold2\u57282020\u5e74\u53d6\u5f97\u7a81\u7834\u4ee5\u6765\uff0c\u5b66\u754c\u5728\u9884\u6d4b\u86cb\u767d\u8d28\u7ed3\u6784\u65b9\u9762\u53d6\u5f97\u4e86\u591a\u5927\u7684\u8fdb\u5c55\uff1f\u5c24\u5176\u662fTransformer\u67b6\u6784\u5728\u5176\u4e2d\u8d77\u5230\u591a\u5927\u4f5c\u7528\uff1f\u8fd9\u4e9b\u6210\u4e3a\u4e86\u65b0\u7684\u95ee\u9898\u3002<\/span><\/p>\n


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\u5728\u7ed3\u6784\u9884\u6d4b\u754c\uff0c\u5e7f\u6cdb\u8ba4\u53ef\u9700\u8981\u8fdb\u884c\u76f2\u76ee\u7ed3\u6784\u9884\u6d4b\u6d4b\u8bd5\uff0c\u4ee5\u5ba2\u89c2\u8bc4\u4f30\u65b0\u7684\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\u65b9\u6cd5\u7684\u6027\u80fd\u3002\u6700\u8fd1\u7ed3\u675f\u7684CASP15\u4f1a\u8bae\u4e3a\u8bc4\u4f30\u8fd9\u4e9b\u65b0\u5174\u65b9\u6cd5\u63d0\u4f9b\u4e86\u4e00\u4e2a\u4f18\u79c0\u7684\u6d4b\u8bd5\u5e73\u53f0\u3002\u65b0\u53d1\u8868\u4e8ePNAS<\/em>\u7684\u4e00\u7bc7\u7814\u7a76\uff0c\u5bf969\u4e2aCASP15\u5355\u94fe\u86cb\u767d\u8d28\u76ee\u6807\u7684\u9884\u6d4b\u5efa\u6a21\u6027\u80fd\u8fdb\u884c\u4e86\u57fa\u51c6\u6d4b\u8bd5\u3002\u9996\u5148\uff0c\u7814\u7a76\u8005\u4e0b\u8f7d\u4e86\u6240\u6709\u65b9\u6cd5\u7684\u5f00\u6e90\u8f6f\u4ef6\u5b9e\u73b0\uff0c\u5e76\u4f7f\u7528\u9ed8\u8ba4\u53c2\u6570\u8bbe\u7f6e\u7684\u5efa\u6a21\u6d41\u7a0b\u8fdb\u884c\u4e86\u5b8c\u5168\u81ea\u52a8\u5316\u7684\u6a21\u5f0f\uff0c\u6ca1\u6709\u4efb\u4f55\u624b\u52a8\u5e72\u9884\u3002\u5176\u6b21\uff0c\u7814\u7a76\u8005\u901a\u8fc7\u76f4\u63a5\u5c06\u5168\u957f\u9884\u6d4b\u4e0e\u5b9e\u9a8c\u5750\u6807\u8fdb\u884c\u6bd4\u8f83\uff0c\u800c\u4e0d\u662f\u5c06\u5176\u5206\u5272\u6210\u57df\uff0c\u6765\u8bc4\u4f30\u5355\u94fe\u9884\u6d4b\u5efa\u6a21\u7684\u51c6\u786e\u6027\u3002\u5bf9\u591a\u57df\u86cb\u767d\u8d28\u8fdb\u884c\u4e86\u989d\u5916\u7684\u9886\u57df\u7ea7\u522b\u5206\u6790\uff0c\u4ee5\u68c0\u67e5\u5404\u4e2a\u9886\u57df\u53ca\u5176\u7ed3\u6784\u7684\u76f8\u5bf9\u51c6\u786e\u6027\u3002\u7b2c\u4e09\uff0c\u7814\u7a76\u8005\u4f7f\u7528\u7684\u662f\u5728CASP15\u4e4b\u524d\u53d1\u5e03\u7684\u9759\u6001\u6570\u636e\u5e93\u3001\u5e93\u548c\u6a21\u578b\u6743\u91cd\uff0c\u6ca1\u6709\u4e2d\u95f4\u66f4\u65b0\u3002<\/span><\/p>\n


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\u8be5\u8bba\u6587\u5c55\u793a\u4e86\u5404\u79cd\u65b9\u6cd5\u7684\u4e3b\u5e72\u51c6\u786e\u6027\u4ee5\u53ca\u5b83\u4eec\u4e4b\u95f4\u4f7f\u7528\u5168\u5c40\u8ddd\u79bb\u6d4b\u8bd5<\/span>\uff08GDT-TS\uff09<\/span>\u6307\u6807\u7684\u5bf9\u6bd4\u7ed3\u679c\uff0c\u5982\u56fe1\u6240\u793a\u3002\u5176\u4e2dAlphaFold2<\/strong>\u4ee5\u6700\u9ad8\u7684\u5e73\u5747GDT-TS\u5f97\u520673.06\u53d6\u5f97\u4e86\u6700\u4f73\u8868\u73b0\uff0c\u660e\u663e\u4f18\u4e8e\u5176\u4ed6\u6240\u6709\u65b9\u6cd5\u3002ESMFold<\/strong>\u5728\u4e3b\u5e72\u5b9a\u4f4d\u65b9\u9762\u8868\u73b0\u51fa\u7b2c\u4e8c\u597d\u7684\u6027\u80fd\uff0c\u5e73\u5747GDT-TS\u5f97\u5206\u4e3a61.62\u3002\u6709\u8da3\u7684\u662f\uff0c\u57fa\u4e8ePLM<\/span>\uff08protein language models\uff0c\u86cb\u767d\u8d28\u8bed\u8a00\u6a21\u578b\uff09<\/span>\u7684ESMFold\u5728\u8d85\u8fc780%\u7684\u60c5\u51b5\u4e0b\u4f18\u4e8e\u57fa\u4e8eMSA<\/span>\uff08multiple sequence alignment\uff0c\u591a\u91cd\u5e8f\u5217\u6bd4\u5bf9\uff09<\/span>\u7684RoseTTAFold\uff0c\u5e76\u83b7\u5f97\u4e86\u66f4\u9ad8\u7684\u5e73\u5747GDT-TS\u5f97\u5206\u3002\u76f8\u6bd4\u4e4b\u4e0b\uff0cAlphaFold2\u5728\u8fd180%\u7684\u60c5\u51b5\u4e0b\u4f18\u4e8eESMFold\u3002\u5728\u8fd9\u4e24\u79cd\u57fa\u4e8ePLM\u7684\u65b9\u6cd5\u4e2d\uff0cESMFold\u5728\u4e3b\u5e72\u5b9a\u4f4d\u65b9\u9762\u7684\u6574\u4f53\u51c6\u786e\u6027\u4f18\u4e8eOmegaFold\u3002<\/span><\/p>\n


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\u5c3d\u7ba1AlphaFold2\u4ee5\u57fa\u4e8eTransformer\u7684\u795e\u7ecf\u7f51\u7edc\u5728\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\u65b9\u9762\u53d6\u5f97\u4e86\u663e\u8457\u8fdb\u5c55\uff0c\u4f46\u8be5\u7814\u7a76\u63ed\u793a\u4e86\u4e24\u4e2a\u6301\u7eed\u5b58\u5728\u7684\u95ee\u9898\u3002\u9996\u5148\uff0c\u5bf9\u4e8e\u5177\u6709\u590d\u6742\u62d3\u6251\u7ed3\u6784\u7684\u5927\u578b\u591a\u57df\u86cb\u767d\u8d28\u7684\u51c6\u786e\u9884\u6d4b\u4ecd\u7136\u5177\u6709\u6311\u6218\u6027\u3002\u5bf9\u4e8e\u5176\u4e2d\u4e00\u4e9b\u76ee\u6807\uff0c\u6ca1\u6709\u4e00\u79cd\u65b9\u6cd5\u80fd\u591f\u51c6\u786e\u9884\u6d4b\u51fa\u9002\u5f53\u7684\u57df\u5b9a\u5411\u548c\u6574\u4f53\u62d3\u6251\u7ed3\u6784\u3002\u901a\u8fc7\u6a21\u62df\u86cb\u767d\u8d28\u95f4\u76f8\u4e92\u4f5c\u7528\u7684\u539f\u5219\u6765\u8c03\u6574Transformer\u6a21\u578b\u7684\u67b6\u6784\uff0c\u53ef\u80fd\u5bf9\u4e8e\u5927\u578b\u591a\u57df\u86cb\u767d\u8d28\u662f\u5fc5\u8981\u7684\u3002\u5176\u6b21\uff0c\u76ee\u524d\u6240\u6709\u65b9\u6cd5\u5728\u4fa7\u94fe\u5b9a\u4f4d\u7684\u51c6\u786e\u6027\u4e0a\u4ecd\u7136\u8f83\u4f4e\u3002\u7ed3\u6784\u9884\u6d4b\u7b97\u6cd5\u5c06\u53d7\u76ca\u4e8e\u51c6\u786e\u7684\u4fa7\u94fe\u6392\u5217\uff0c\u8fd9\u53ef\u80fd\u8981\u901a\u8fc7\u5728\u795e\u7ecf\u67b6\u6784\u4e2d\u52a0\u5165\u4fa7\u94fe\u4f18\u5316\u6765\u5b9e\u73b0\u3002<\/span><\/p>\n


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\u4f5c\u8005\u63d0\u51fa\uff0c\u7ed3\u5408MSA<\/span>\uff08multiple sequence alignment\uff0c\u591a\u91cd\u5e8f\u5217\u6bd4\u5bf9\uff09<\/span>\u548cPLM<\/span>\uff08protein language models\uff0c\u86cb\u767d\u8d28\u8bed\u8a00\u6a21\u578b\uff09<\/span>\u4e24\u8005\u7684\u4f18\u52bf\uff0c\u53ef\u80fd\u662f\u8fdb\u4e00\u6b65\u63a8\u8fdb\u7ed3\u6784\u751f\u7269\u5b66\u4e2d\u86cb\u767d\u8d28\u9884\u6d4b\u6a21\u578b\u7684\u9014\u5f84\u3002<\/span><\/p>\n


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\u56fe1 \u5bf9CASP15\u6570\u636e\u96c6\u4e0a\u6700\u5148\u8fdb\u7684\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\u65b9\u6cd5\u8fdb\u884c\u6027\u80fd\u57fa\u51c6\u6d4b\u8bd5\u3002\uff08A\uff09GDT-TS\u5f97\u5206\u6bd4\u8f83\u3002\u865a\u7ebf\u8868\u793a\u5e73\u5747\u6027\u80fd\uff0c\u5de6\u4e0a\u89d2\u7684\u767e\u5206\u6bd4\u8868\u793ay\u8f74\u4e0a\u7684\u65b9\u6cd5\u4f18\u4e8ex\u8f74\u4e0a\u7684\u65b9\u6cd5\uff0c\u53f3\u4e0b\u89d2\u5219\u76f8\u53cd\u3002\uff08B\uff09Grishin\u56fe\u5206\u6790\u3002\uff08C\uff09\u57df\u7ea7GDT-TS\u5f97\u5206\u4e0e\u57df\u957f\u5ea6\u7684\u5173\u7cfb\uff0c\u63d2\u56fe\u663e\u793a\u957f\u5ea6\u5c0f\u4e8e750\u4e2a\u6b8b\u57fa\u7684\u57df\u3002\u7ebf\u8868\u793a\u6570\u636e\u7684\u7ebf\u6027\u62df\u5408\u3002\uff08D\uff09\u4e09\u4e2a\u4ee3\u8868\u6027\u7684CASP15\u76ee\u6807\uff0c\u9884\u6d4b\u7ed3\u679c\uff08\u5f69\u8679\u8272\uff09\u4e0e\u5b9e\u9a8c\u7ed3\u6784\uff08\u7070\u8272\uff09\u7684\u53e0\u52a0\u3002\u7c97\u4f53\u6570\u5b57\u8868\u793a\u6700\u4f73\u6027\u80fd\u3002\uff08E\uff09\u6574\u4f53\u62d3\u6251\u9884\u6d4b\u6027\u80fd\uff0c\u4ee5%TM-score >0.5\u4e3a\u6307\u6807\u3002\uff08F\uff09\u57fa\u4e8eMSA\u7684\u65b9\u6cd5\u7684lDDT\u5f97\u5206\u4e0e\u4ee5Neff\u7684\u5bf9\u6570\u4e3a\u5355\u4f4d\u7684MSA\u6df1\u5ea6\u7684\u5173\u7cfb\u3002\u7ebf\u8868\u793a\u6570\u636e\u7684\u7ebf\u6027\u62df\u5408\u3002\uff08G\uff09lDDT\u5f97\u5206\u4e0e\u86cb\u767d\u8d28\u76ee\u6807\u957f\u5ea6\u7684\u5173\u7cfb\uff0c\u63d2\u56fe\u663e\u793a\u957f\u5ea6\u5c0f\u4e8e750\u4e2a\u6b8b\u57fa\u7684\u76ee\u6807\u3002\u7ebf\u8868\u793a\u6570\u636e\u7684\u7ebf\u6027\u62df\u5408\u3002\uff08H\uff09Ramachandran\u56fe\u5206\u6790\u3002\u989c\u8272\u4ee3\u7801\u4ece\u84dd\u8272\u5230\u7ea2\u8272\u8868\u793a\u4f4e\u5bc6\u5ea6\u5230\u9ad8\u5bc6\u5ea6\u3002(I) MolProbity\u5f97\u5206\u5206\u5e03\u3002(J) GDC-SC\u5f97\u5206\u4e0eA\u7c7b\u4f3c\u7684\u6bd4\u8f83\u3002<\/span><\/span><\/section>\n

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\u5927\u6a21\u578b\u4e0e\u751f\u7269\u533b\u5b66\uff1a<\/strong><\/p>\n

AI + Science\u7b2c\u4e8c\u5b63\u8bfb\u4e66\u4f1a\u542f\u52a8<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n


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\u5927\u6a21\u578b\u4e0e\u751f\u7269\u533b\u5b66\uff1aAI + Science\u7b2c\u4e8c\u5b63\u8bfb\u4e66\u4f1a\u542f\u52a8<\/a><\/span>
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\u200d<\/span>1. <\/strong>Science \u524d\u6cbf\uff1a\u7a7a\u95f4\u7ec4\u5b66\u4e3a\u65b0\u4e00\u4ee3\u79d1\u5b66\u53d1\u73b0\u8d4b\u80fd<\/a><\/strong><\/span><\/strong><\/strong><\/section>\n
2.<\/strong> Science\u524d\u6cbf\uff1a\u5927\u8bed\u8a00\u6a21\u578b\u6d8c\u73b0\u6f14\u5316\u4fe1\u606f\uff0c\u52a0\u901f\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b<\/a><\/strong><\/span><\/strong><\/section>\n
3. <\/strong><\/strong>Science \u901f\u9012\uff1a\u5927\u8bed\u8a00\u6a21\u578b\u5bf9\u86cb\u767d\u8d28\u7ed3\u6784\u8fdb\u884c\u6f14\u5316\u5c3a\u5ea6\u9884\u6d4b<\/a><\/strong><\/strong><\/span><\/strong><\/strong><\/section>\n
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4. <\/strong><\/strong><\/span>\u5f20\u6c5f\uff1a\u7b2c\u4e09\u4ee3\u4eba\u5de5\u667a\u80fd\u6280\u672f\u57fa\u7840\u2014\u2014\u4ece\u53ef\u5fae\u5206\u7f16\u7a0b\u5230\u56e0\u679c\u63a8\u7406 | \u96c6\u667a\u5b66\u56ed\u5168\u65b0\u8bfe\u7a0b<\/a><\/strong><\/strong><\/span><\/section>\n
5. <\/strong><\/strong>\u52a0\u5165\u96c6\u667a\u5b66\u56edVIP\uff0c\u83b7\u5f9720\u5468\u5e74\u201c\u6d8c\u73b0\u201d\u5b66\u672f\u5e74\u4f1a\u5165\u573a\u5238\uff01<\/a><\/strong><\/strong><\/strong><\/strong><\/span><\/section>\n
6. <\/strong>\u52a0\u5165\u96c6\u667a\uff0c\u4e00\u8d77\u590d\u6742\uff01<\/strong><\/span><\/a><\/section>\n

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\u70b9\u51fb\u201c\u9605\u8bfb\u539f\u6587\u201d\uff0c\u62a5\u540d\u8bfb\u4e66\u4f1a<\/strong><\/strong><\/span><\/strong><\/section>\n

<\/mp-style-type><\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

\u5173\u952e\u8bcd\uff1aTransformer\u795e\u7ecf\u7f51\u7edc\uff0c\u86cb\u767d\u8d28\u7ed3\u6784\u9884\u6d4b\uff0c\u7ed3\u6784\u751f\u7269\u5b66 \u8bba\u6587\u9898\u76ee\uff1aThe transformative power of transformers in protein structure prediction \u671f\u520a\u540d\u79f0\uff1aPNAS \u6591\u56fe\u5730\u5740\uff1ahttps:\/\/pattern.swarma….<\/p>\n","protected":false},"author":0,"featured_media":44557,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"special":[],"_links":{"self":[{"href":"https:\/\/swarma.org\/index.php?rest_route=\/wp\/v2\/posts\/44561"}],"collection":[{"href":"https:\/\/swarma.org\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/swarma.org\/index.php?rest_route=\/wp\/v2\/types\/post"}],"replies":[{"embeddable":true,"href":"https:\/\/swarma.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=44561"}],"version-history":[{"count":0,"href":"https:\/\/swarma.org\/index.php?rest_route=\/wp\/v2\/posts\/44561\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/swarma.org\/index.php?rest_route=\/wp\/v2\/media\/44557"}],"wp:attachment":[{"href":"https:\/\/swarma.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=44561"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/swarma.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=44561"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/swarma.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=44561"},{"taxonomy":"special","embeddable":true,"href":"https:\/\/swarma.org\/index.php?rest_route=%2Fwp%2Fv2%2Fspecial&post=44561"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}