{"id":67100,"date":"2026-11-14T19:46:18","date_gmt":"2026-11-14T11:46:18","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=67100"},"modified":"2026-11-14T20:45:47","modified_gmt":"2026-11-14T12:45:47","slug":"alphafold3-protein-interface-chain-pair-iptm-pae","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/alphafold3-protein-interface-chain-pair-iptm-pae\/","title":{"rendered":"AlphaFold 3 \u4e24\u6761\u94fe\u90fd\u5f88\u84dd\uff0c\u600e\u4e48\u5224\u65ad\u5b83\u4eec\u4e4b\u95f4\u7684\u754c\u9762\u9760\u4e0d\u9760\u8c31\uff1f"},"content":{"rendered":"
\n

\u6253\u5f00\u4e00\u4efd\u53cc\u94fe\u86cb\u767d\u7684\u9884\u6d4b\u7ed3\u6784\uff0c\u94fe A \u548c\u94fe B \u90fd\u6298\u5f97\u50cf\u6a21\u50cf\u6837\u3002\u6309\u7f6e\u4fe1\u5ea6\u7740\u8272\u540e\uff0c\u5927\u90e8\u5206\u533a\u57df\u53c8\u662f\u6df1\u84dd\u8272\uff0c\u5f88\u5bb9\u6613\u987a\u624b\u622a\u5f20\u56fe\uff0c\u5199\u4e0b\u201c\u4e24\u79cd\u86cb\u767d\u5f62\u6210\u7a33\u5b9a\u590d\u5408\u7269\u201d\u3002\u4f46\u505a\u7a81\u53d8\u5b9e\u9a8c\u7684\u4eba\u8fd8\u8981\u77e5\u9053\u4e00\u4e2a\u66f4\u5177\u4f53\u7684\u95ee\u9898\u3002\u628a\u94fe A \u56fa\u5b9a\u5728\u8fd9\u91cc\uff0c\u94fe B \u771f\u6709\u628a\u63e1\u843d\u5728\u56fe\u4e0a\u8fd9\u4e00\u9762\u5417\uff1f\u4e24\u6761\u94fe\u5404\u81ea\u6298\u5f97\u597d\uff0c\u4e0e\u5b83\u4eec\u5f7c\u6b64\u7684\u4f4d\u7f6e\u53ef\u4e0d\u53ef\u9760\uff0c\u9700\u8981\u770b\u4e0d\u540c\u7684\u8f93\u51fa\u3002<\/p>\n

\u5148\u628a\u67e5\u770b\u5668\u5207\u6362\u5230\u6309 pLDDT \u7740\u8272\u5e76\u770b\u6e05\u56fe\u4f8b\u3002\u6709\u4e9b\u8f6f\u4ef6\u7528\u4e0d\u540c\u989c\u8272\u533a\u5206\u94fe\uff0c\u6216\u6309\u4e8c\u7ea7\u7ed3\u6784\u7740\u8272\uff0c\u5c4f\u5e55\u4e0a\u7684\u84dd\u8272\u672c\u8eab\u6ca1\u6709\u56fa\u5b9a\u542b\u4e49\u3002\u4ee5\u4e0b\u8ba8\u8bba\u7684\u662f\u4e24\u6761\u666e\u901a\u86cb\u767d\u94fe\u3002\u82e5\u7814\u7a76\u7684\u662f\u542b\u5c0f\u5206\u5b50\u6216\u4fee\u9970\u57fa\u56e2\u7684\u590d\u5408\u7269\uff0c\u6a21\u578b\u4f7f\u7528\u7684 token \u4e0e\u6c28\u57fa\u9178\u6b8b\u57fa\u4e0d\u603b\u662f\u4e00\u4e00\u5bf9\u5e94\uff0c\u4e0d\u80fd\u76f4\u63a5\u7167\u642c\u6b8b\u57fa\u7f16\u53f7\u3002<\/p>\n

\u6253\u5f00\u540c\u4e00\u4e2a\u9884\u6d4b\u6837\u672c\u7684\u4e09\u4e2a\u6587\u4ef6<\/h2>\n

\u5728\u672c\u5730 AlphaFold 3 \u7684\u8f93\u51fa\u91cc\uff0c\u5148\u9009\u5b9a\u4e00\u4e2a\u79cd\u5b50\u548c\u91c7\u6837\u7f16\u53f7\uff0c\u6253\u5f00\u5bf9\u5e94\u76ee\u5f55\u4e2d\u7684 *_model.cif<\/code>\u3001*_summary_confidences.json<\/code> \u548c *_confidences.json<\/code>\u3002\u7b2c\u4e00\u4e2a\u7ed9\u4e09\u7ef4\u5750\u6807\uff0c\u7b2c\u4e8c\u4e2a\u7ed9\u6574\u5957\u7ed3\u6784\u53ca\u94fe\u5bf9\u7684\u6c47\u603b\u5206\u6570\uff0c\u7b2c\u4e09\u4e2a\u542b\u9010\u539f\u5b50\u7684\u5c40\u90e8\u7f6e\u4fe1\u5ea6\u53ca\u9010 token \u7684\u8bef\u5dee\u77e9\u9635\u3002\u6839\u76ee\u5f55\u653e\u7684\u662f\u6574\u5957\u9884\u6d4b\u4e2d\u6392\u540d\u6700\u9ad8\u7684\u6837\u672c\u3002\u5982\u679c\u5728\u67e5\u770b\u5668\u91cc\u6253\u5f00\u4e86\u53e6\u4e00\u4e2a\u6837\u672c\uff0c\u5c31\u8981\u8fde\u540c\u5b83\u7684\u4e24\u4e2a JSON \u4e00\u8d77\u6362\u8fc7\u53bb\uff0c\u5426\u5219\u53ef\u80fd\u4f1a\u62ff\u4e00\u4e2a\u59ff\u52bf\u89e3\u91ca\u53e6\u4e00\u4e2a\u59ff\u52bf\u7684\u5206\u6570\u3002AlphaFold 3 \u5b98\u65b9\u8f93\u51fa\u8bf4\u660e<\/a><\/p>\n

\n\n\n\n\n\n\n\n
\u60f3\u56de\u7b54\u7684\u95ee\u9898<\/th>\n\u53bb\u54ea\u91cc\u770b<\/th>\n\u8bfb\u6570\u65f6\u8981\u8bb0\u4f4f<\/th>\n<\/tr>\n<\/thead>\n
\u67d0\u6bb5\u4e3b\u94fe\u6216\u9644\u8fd1\u539f\u5b50\u7684\u4f4d\u7f6e\u6709\u591a\u53ef\u9760<\/td>\n\u6309 pLDDT \u7740\u8272\u7684\u7ed3\u6784\uff0c\u6216\u8be6\u7ec6 JSON \u7684 atom_plddts<\/code><\/td>\n\u5c40\u90e8\u8bc4\u5206\u9ad8\uff0c\u652f\u6301\u8be5\u5904\u5c40\u90e8\u51e0\u4f55\u3002\u53e6\u4e00\u6761\u94fe\u7684\u6446\u653e\u8981\u5355\u72ec\u68c0\u67e5<\/td>\n<\/tr>\n
A\u3001B \u7684\u76f8\u5bf9\u6446\u653e\u6709\u591a\u53ef\u9760<\/td>\n\u6c47\u603b JSON \u7684 chain_pair_iptm<\/code><\/td>\n\u6309\u94fe\u987a\u5e8f\u627e A\u3001B \u5bf9\u5e94\u7684\u975e\u5bf9\u89d2\u5143\u7d20\u3002\u5bf9\u89d2\u5143\u7d20\u53cd\u6620\u5404\u94fe\u81ea\u8eab\u7684 pTM<\/td>\n<\/tr>\n
\u54ea\u4e9b\u7247\u6bb5\u4e4b\u95f4\u7684\u76f8\u5bf9\u4f4d\u7f6e\u8f83\u786e\u5b9a<\/td>\n\u8be6\u7ec6 JSON \u7684 pae<\/code> \u548c token_chain_ids<\/code><\/td>\n\u8bef\u5dee\u4ee5\u57c3\u4e3a\u5355\u4f4d\uff0c\u6570\u503c\u8f83\u5c0f\u8868\u793a\u76f8\u5bf9\u4f4d\u7f6e\u66f4\u6709\u628a\u63e1\uff0c\u8981\u6807\u51fa\u94fe\u8fb9\u754c<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

pLDDT \u7684\u53d6\u503c\u8303\u56f4\u662f\u96f6\u5230\u4e00\u767e\u3002\u5728\u4e24\u94fe\u90fd\u6298\u53e0\u826f\u597d\u3001\u4f46\u5b83\u4eec\u4e4b\u95f4\u6ca1\u6709\u8db3\u591f\u4fe1\u606f\u9650\u5b9a\u65b9\u5411\u7684\u60c5\u51b5\u4e0b\uff0c\u5927\u90e8\u5206\u539f\u5b50\u4ecd\u7136\u53ef\u4ee5\u83b7\u5f97\u9ad8\u7684\u5c40\u90e8\u8bc4\u5206\u3002ipTM \u5173\u6ce8\u4e9a\u57fa\u95f4\u76f8\u5bf9\u4f4d\u7f6e\u7684\u53ef\u4fe1\u5ea6\u3002\u5728\u591a\u94fe\u4f53\u7cfb\u91cc\uff0c\u6574\u4f53 ipTM \u53ef\u80fd\u63a9\u76d6\u67d0\u4e00\u5bf9\u94fe\u7684\u5f31\u8bc1\u636e\uff0c\u6240\u4ee5\u7814\u7a76\u6307\u5b9a\u7684\u4e24\u4e2a\u86cb\u767d\u65f6\u5e94\u8bfb\u94fe\u5bf9\u5206\u6570\u3002\u67e5\u770b\u5668\u82e5\u628a\u8fd9\u4e2a\u5206\u6570\u663e\u793a\u6210\u5c0f\u6570\uff0c\u4e5f\u4e0d\u8981\u628a\u5b83\u6362\u7b97\u6210\u201c\u4e24\u79cd\u86cb\u767d\u6709\u767e\u5206\u4e4b\u591a\u5c11\u6982\u7387\u7ed3\u5408\u201d\u3002EMBL-EBI \u7684\u590d\u5408\u7269\u7ed3\u679c\u8bfb\u56fe\u6559\u7a0b<\/a><\/p>\n

\u5728 PAE \u56fe\u4e0a\u627e\u5230\u94fe\u4e0e\u94fe\u4e4b\u95f4\u7684\u683c\u5b50<\/h2>\n

\u628a A \u653e\u5728\u5750\u6807\u8f74\u524d\u534a\u6bb5\u3001B \u653e\u5728\u540e\u534a\u6bb5\uff0c\u6574\u5f20\u56fe\u4fbf\u5206\u6210\u56db\u5757\u3002\u5de6\u4e0a\u548c\u53f3\u4e0b\u5bf9\u5e94\u5404\u94fe\u5185\u90e8\uff0c\u53e6\u5916\u4e24\u5757\u624d\u63cf\u8ff0\u8de8\u94fe\u7684\u76f8\u5bf9\u4f4d\u7f6e\u3002PAE \u7684\u76f4\u89c2\u610f\u601d\u662f\uff0c\u7528\u67d0\u4e00\u4e2a\u4f4d\u7f6e\u4f5c\u4e3a\u5bf9\u9f50\u53c2\u7167\u540e\uff0c\u6a21\u578b\u4f30\u8ba1\u53e6\u4e00\u4e2a\u4f4d\u7f6e\u53ef\u80fd\u504f\u79bb\u591a\u5c11\u3002\u8c03\u6362\u53c2\u7167\u70b9\uff0c\u4f30\u8ba1\u8bef\u5dee\u672a\u5fc5\u76f8\u540c\uff0c\u6240\u4ee5\u8981\u628a\u4e0a\u4e0b\u4e24\u4e2a\u8de8\u94fe\u533a\u57df\u90fd\u770b\u4e00\u773c\u3002\u4e0d\u540c\u753b\u56fe\u7a0b\u5e8f\u4e5f\u4f1a\u6362\u8272\uff0c\u5148\u8bfb\u8272\u6761\u4e0a\u6807\u7684\u6570\u503c\uff0c\u522b\u8bb0\u6b7b\u201c\u6df1\u8272\u624d\u597d\u201d\u3002<\/p>\n

\u8bfb\u8005\u53ef\u4ee5\u5148\u5728\u7ed3\u6784\u4e2d\u9009\u4e2d\u81ea\u5df1\u5173\u5fc3\u7684\u63a5\u89e6\u9762\uff0c\u518d\u56de\u56fe\u91cc\u770b\u76f8\u5173\u7247\u6bb5\u3002\u4e00\u6574\u6761\u957f\u94fe\u7684\u67d4\u6027\u5c3e\u90e8\u53ef\u80fd\u6709\u5f88\u9ad8\u7684\u8bef\u5dee\uff0c\u4e0d\u5b9c\u636e\u6b64\u5426\u5b9a\u53e6\u4e00\u7aef\u6298\u53e0\u7ed3\u6784\u57df\u4e0a\u7684\u754c\u9762\u3002\u53cd\u8fc7\u6765\uff0c\u8de8\u94fe\u533a\u57df\u5076\u7136\u51fa\u73b0\u4e00\u4e2a\u4f4e\u8bef\u5dee\u683c\u5b50\uff0c\u4e5f\u4e0d\u8db3\u4ee5\u5708\u5b9a\u6574\u7247\u754c\u9762\u3002\u6bd4\u8f83\u6709\u89e3\u91ca\u529b\u7684\u662f\u4e00\u7ec4\u76f8\u90bb\u6b8b\u57fa\u90fd\u7ed9\u51fa\u8f83\u4f4e\u7684\u8de8\u94fe\u8bef\u5dee\uff0c\u800c\u4e14\u8fd9\u4e9b\u6b8b\u57fa\u5728\u4e09\u7ef4\u6a21\u578b\u91cc\u786e\u5b9e\u4f4d\u4e8e\u4e24\u6761\u94fe\u9760\u8fd1\u7684\u8868\u9762\u3002PAE \u7684\u5355\u4f4d\u867d\u7136\u662f\u57c3\uff0c\u683c\u5b50\u91cc\u7684\u6570\u5b57\u6307\u9884\u6d4b\u4f4d\u7f6e\u7684\u8bef\u5dee<\/strong>\u3002\u5b9e\u9645\u63a5\u89e6\u8ddd\u79bb\u5e94\u56de\u5230\u5750\u6807\u4e2d\u6d4b\u91cf\u3002<\/p>\n

\"\u53cc\u94fe\u86cb\u767d
PAE \u5206\u533a\u793a\u610f\u3002\u989c\u8272\u7528\u4e8e\u533a\u5206\u533a\u57df\uff0c\u672a\u7f16\u7801\u4efb\u4f55\u5b9e\u9645\u86cb\u767d\u7684 PAE \u6570\u503c\u3002<\/figcaption><\/figure>\n

\u7528\u5341\u51e0\u884c Python \u4eb2\u81ea\u6838\u5bf9\u65b9\u5411<\/h2>\n

\u4e0b\u9762\u662f\u56db\u4e2a token \u7684\u6559\u5b66\u77e9\u9635\uff0c\u6bcf\u6761\u94fe\u53ea\u6709\u4e24\u4e2a\u4f4d\u7f6e\u3002\u8fd9\u4e2a\u6781\u7b80\u4f8b\u5b50\u4e0d\u4ee3\u8868\u4efb\u4f55\u771f\u5b9e\u86cb\u767d\uff0c\u53ea\u7528\u6765\u68c0\u67e5\u884c\u5217\u65b9\u5411\u548c\u5355\u4f4d\u3002\u6309\u5b98\u65b9\u672c\u5730\u8f93\u51fa\u5b9a\u4e49\uff0c\u7b2c\u4e00\u4e2a\u4e0b\u6807\u662f\u7528\u4e8e\u5bf9\u9f50\u7684\u53c2\u7167 token\uff0c\u7b2c\u4e8c\u4e2a\u4e0b\u6807\u662f\u88ab\u8bc4\u4ef7\u4f4d\u7f6e\u3002\u4e24\u6b21\u53d6\u5757\u53ea\u4ea4\u6362\u884c\u548c\u5217\u7684\u94fe\u540d\uff0c\u4ee3\u7801\u53ea\u7528 Python \u6807\u51c6\u5e93\u5373\u53ef\u8fd0\u884c\u3002<\/p>\n

from statistics import median\r\n\r\nd = {"token_chain_ids": ["A", "A", "B", "B"],\r\n     "pae": [[0, 1, 9, 11], [1, 0, 10, 12],\r\n             [12, 10, 0, 1], [14, 12, 1, 0]]}\r\nids = d["token_chain_ids"]\r\nfor ref, target in [("A", "B"), ("B", "A")]:\r\n    block = [d["pae"][i][j]\r\n             for i, a in enumerate(ids) if a == ref\r\n             for j, b in enumerate(ids) if b == target]\r\n    print(ref, "->", target, median(block))\r\n<\/code><\/pre>\n
\u56fa\u5b9a A \u8bc4\u4ef7 B\uff0c\u56db\u4e2a\u6570\u662f 9\u300111\u300110\u300112\uff0c\u4e2d\u4f4d\u6570 10.5 \u57c3\u3002\u56fa\u5b9a B \u8bc4\u4ef7 A\uff0c\u4e2d\u4f4d\u6570\u662f 12 \u57c3\u3002\u5bf9\u81ea\u5df1\u7684\u6a21\u578b\uff0c\u53ef\u4ee5\u7528 json.load<\/code> \u8bfb\u53d6\u8be6\u7ec6\u7f6e\u4fe1\u5ea6\u6587\u4ef6\u5e76\u66ff\u6362\u4ee3\u7801\u4e2d\u7684 d<\/code>\uff0c\u518d\u628a A\u3001B \u6539\u4e3a\u6587\u4ef6\u4e2d\u7684\u5b9e\u9645\u94fe\u540d\u3002\u82e5\u76ee\u7684\u662f\u5b9a\u4f4d\u63a5\u89e6\u9762\uff0c\u8fd8\u5e94\u53ea\u9009\u7ed3\u6784\u4e2d\u63a5\u89e6\u7247\u6bb5\u5bf9\u5e94\u7684\u884c\u5217\uff0c\u4fdd\u7559\u6b8b\u57fa\u7f16\u53f7\u3002\u6574\u6761\u94fe\u5bf9\u7684\u4e2d\u4f4d\u6570\u9002\u5408\u505a\u65b9\u5411\u68c0\u67e5\uff0c\u957f\u94fe\u4e0a\u5927\u91cf\u8fdc\u79bb\u754c\u9762\u7684\u4f4d\u70b9\u4f1a\u6df9\u6ca1\u4e00\u4e2a\u5c0f\u754c\u9762\uff0c\u4e0d\u80fd\u62ff\u8fd9\u4e2a\u4e2d\u4f4d\u6570\u505a\u7edf\u4e00\u7684\u7b5b\u9009\u9608\u503c\u3002<\/p>\n
\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u5750\u6807\u7ed3\u6784\u91cc\u7684\u77ed\u80bd\u53eb U\uff0c\u7f6e\u4fe1\u5ea6\u77e9\u9635\u5374\u53eb B<\/h2>\n
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