{"id":113,"date":"2025-03-27T02:58:01","date_gmt":"2025-03-27T02:58:01","guid":{"rendered":"http:\/\/drtem.cn\/?p=113"},"modified":"2025-08-08T14:22:22","modified_gmt":"2025-08-08T06:22:22","slug":"%e8%8b%8f%e5%b7%9e%e5%be%b7%e9%94%90%e7%89%b9%e5%bc%80%e6%ba%90%e8%bd%af%e4%bb%b6fep-spell-abfe-%e6%ad%a3%e5%bc%8f%e5%8f%91%e5%b8%83%e5%9c%a8%e7%be%8e%e5%9b%bd%e5%8c%96%e5%ad%a6%e4%bc%9a%e6%97%97","status":"publish","type":"post","link":"https:\/\/www.drtem.cn\/en\/2025\/03\/27\/%e8%8b%8f%e5%b7%9e%e5%be%b7%e9%94%90%e7%89%b9%e5%bc%80%e6%ba%90%e8%bd%af%e4%bb%b6fep-spell-abfe-%e6%ad%a3%e5%bc%8f%e5%8f%91%e5%b8%83%e5%9c%a8%e7%be%8e%e5%9b%bd%e5%8c%96%e5%ad%a6%e4%bc%9a%e6%97%97\/","title":{"rendered":"DRTem's open-source software, FEP-SPell-ABFE, has been officially published in JCIM"},"content":{"rendered":"<p><span style=\"color: #5e5e5e;\">\u7ed3\u5408\u81ea\u7531\u80fd\u7684\u8ba1\u7b97\uff0c\u5c24\u5176\u662f\u9488\u5bf9\u86cb\u767d-\u914d\u4f53\u590d\u5408\u7269\u4f53\u7cfb\uff0c\u662f\u8ba1\u7b97\u5316\u5b66\u9886\u57df\u7684\u4e00\u4e2a\u91cd\u8981\u7814\u7a76\u65b9\u5411\u3002\u70bc\u91d1\u672f\u81ea\u7531\u80fd\u6a21\u62df\uff08Alchemical Free Energy Simulations\uff09\u6280\u672f\u88ab\u4e1a\u5185\u8ba4\u4e3a\u662f\u8ba1\u7b97\u7ed3\u5408\u81ea\u7531\u80fd\u6700\u7cbe\u786e\u7684\u65b9\u6cd5\u3002\u8be5\u6280\u672f\u901a\u8fc7\u5728\u59cb\u672b\u70ed\u529b\u5b66\u6001\u4e4b\u95f4\u589e\u52a0\u4e00\u7cfb\u5217\u865a\u62df\u7684\u4e2d\u95f4\u6001\uff0c\u4ece\u800c\u5b9e\u73b0\u7f13\u6162\u7684\u6f14\u53d8\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u7edd\u5bf9\u7ed3\u5408\u81ea\u7531\u80fdABFE\uff08Absolute Binding Free Energy\uff09\u8ba1\u7b97\u65b9\u6cd5\u901a\u8fc7\u53cc\u89e3\u8026\uff08double-decoupling\uff09\u5c06\u914d\u4f53\u5206\u5b50\u8f6c\u53d8\u6210\u4e0d\u4f1a\u88ab\u5468\u56f4\u73af\u5883\uff08\u6eb6\u5242\u5316\u73af\u5883\u548c\u7ed3\u5408\u4f4d\u70b9\uff09\u6240\u611f\u77e5\u7684\u865a\u62df\u5206\u5b50\uff0c\u8bc4\u4f30\u914d\u4f53\u4e0e\u9776\u86cb\u767d\u4e4b\u95f4\u7684\u7ed3\u5408\u81ea\u7531\u80fd\u3002\u4e0e\u76f8\u5bf9\u7ed3\u5408\u81ea\u7531\u80fd\uff08RBFE\uff09\u4e0d\u540c\uff0cABFE\u8ba1\u7b97\u4e0d\u4f9d\u8d56\u4e8e\u914d\u4f53\u4e4b\u95f4\u7684\u7ed3\u6784\u76f8\u4f3c\u6027\uff0c\u56e0\u6b64\u9002\u7528\u4e8e\u66f4\u5e7f\u6cdb\u7684\u5206\u5b50\u81ea\u7531\u80fd\u8ba1\u7b97\u573a\u666f\u3002\u7136\u800c\uff0c\u4e0eRBFE\u76f8\u6bd4\uff0c\u8ba1\u7b97ABFE\u8fd8\u9700\u8981\u989d\u5916\u7684\u6b65\u9aa4\uff0c\u5982\u5f15\u5165\u6216\u6d88\u9664\u86cb\u767d\u8d28\u548c\u914d\u4f53\u4e4b\u95f4\u7684\u7ea6\u675f\uff0c\u8fd9\u4f7f\u6a21\u62df\u534f\u8bae\u53d8\u5f97\u590d\u6742\uff0c\u5e76\u589e\u52a0\u4e86\u8ba1\u7b97\u9700\u6c42\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u8fd1\u65e5\uff0c\u82cf\u5dde\u5fb7\u9510\u7279\u516c\u53f8\u8054\u5408\u534e\u4e1c\u5e08\u8303\u5927\u5b66\u6885\u6654\u6559\u6388\u8bfe\u9898\u7ec4\u5728<strong><b>\u300aJournal\u00a0of\u00a0Chemical\u00a0Information\u00a0and\u00a0Modeling\u300b<\/b><\/strong><strong><b>\u671f\u520a\u4e0a\u6b63\u5f0f\u53d1\u5e03\u4e86\u5171\u540c\u7814\u53d1\u7684\u81ea\u52a8\u5316\u9884\u6d4bABFE\u7684\u8ba1\u7b97\u5de5\u5177<\/b><\/strong><a style=\"color: #5e5e5e;\" href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c01986\"><strong><u><b>FEP-SPell-ABFE<\/b><\/u><\/strong><\/a><strong><em><b><i>\uff08<\/i><\/b><\/em><\/strong><strong><em><u><b><i>https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c01986<\/i><\/b><\/u><\/em><\/strong><strong><em><b><i>\uff09<\/i><\/b><\/em><\/strong>\uff0c\u8be5\u5de5\u5177\u63d0\u4f9b\u4e86\u4e00\u5957\u9ad8\u6548\u3001\u81ea\u52a8\u5316\u7684ABFE\u8ba1\u7b97\u6d41\u7a0b\uff0c\u80fd\u591f\u8f7b\u91cf\u5316\u5730\u90e8\u7f72\u5728\u9ad8\u6027\u80fd\u8ba1\u7b97\u96c6\u7fa4\u4e0a\uff0c\u4e3a\u7ed3\u6784\u591a\u6837\u7684\u914d\u4f53\u5206\u5b50\u63d0\u4f9b\u4e86\u66f4\u52a0\u7075\u6d3b\u3001\u7cbe\u51c6\u7684\u7ed3\u5408\u81ea\u7531\u80fd\u9884\u6d4b\u65b9\u6848\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><strong><b>FEP-SPell-ABFE<\/b><\/strong>\u00a0\u662f\u4e00\u6b3e\u57fa\u4e8e Python \u7684\u5f00\u6e90\u81ea\u52a8\u5316\u5de5\u4f5c\u6d41\uff0c\u4e13\u4e3a\u8ba1\u7b97\u836f\u7269\u5206\u5b50\u4e0e\u9776\u86cb\u767d\u7684\u7edd\u5bf9\u7ed3\u5408\u81ea\u7531\u80fd\uff08ABFE\uff09\u8bbe\u8ba1\u3002\u8be5\u5de5\u5177\u5927\u5e45\u964d\u4f4e\u4e86\u8ba1\u7b97\u51c6\u5907\u7684\u5de5\u4f5c\u91cf\uff0c\u80fd\u591f\u7b80\u5355\u5feb\u901f\u5730\u9884\u6d4b\u5019\u9009\u5206\u5b50\u7684\u7ed3\u5408\u4eb2\u548c\u529b\u3002\u64cd\u4f5c\u7b80\u4fbf\uff0c\u7528\u6237\u4ec5\u9700\u51c6\u5907\u4e09\u4e2a\u5173\u952e\u6587\u4ef6\u5373\u53ef\u5f00\u5c55\u8ba1\u7b97\uff1a<\/span><\/p>\n<ul>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>\u86cb\u767d\u53d7\u4f53\u7ed3\u6784\u6587\u4ef6\uff08PDB\u683c\u5f0f\uff09<\/b><\/strong><\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>\u5019\u9009\u914d\u4f53\u5206\u5b50\u6587\u4ef6\uff08SDF\u683c\u5f0f\uff09<\/b><\/strong><\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>\u7ba1\u7406\u5de5\u4f5c\u6d41\u548c\u5206\u5b50\u52a8\u529b\u5b66\u6a21\u62df\u53c2\u6570\u7684<\/b><\/strong><strong><b>\u914d\u7f6e\u6587\u4ef6\uff08yaml\uff09<\/b><\/strong><\/span><\/li>\n<\/ul>\n<p><span style=\"color: #5e5e5e;\">\u7528\u6237\u53ef\u6839\u636e\u9700\u6c42\u7075\u6d3b\u8c03\u6574\u914d\u7f6e\u6587\u4ef6config.yaml\uff0c\u901a\u5e38\u53ea\u9700\u7b80\u5355\u4fee\u6539\u76f8\u5173\u914d\u7f6e\uff0c\u5373\u53ef\u4e00\u952e\u63d0\u4ea4\u4efb\u52a1\uff08\u53c2\u89c1\u540e\u6587\u6d41\u7a0b\u793a\u4f8b\uff09\uff0c\u7a0b\u5e8f\u5c06\u81ea\u52a8\u6267\u884c\u6574\u4e2a\u6a21\u62df\u6d41\u7a0b\uff0c\u5e76\u751f\u6210\u5305\u542b\u7ed3\u5408\u81ea\u7531\u80fd\u6570\u636e\u7684CSV\u6587\u4ef6\u3002\u6b64\u5916\uff0c\u8be5\u5de5\u5177\u4f9d\u6258\u00a0SLURM \u8ba1\u7b97\u8d44\u6e90\u7ba1\u7406\u7cfb\u7edf\uff0c\u53ef\u5b9e\u73b0\u8de8\u6a21\u5757\u7684\u81ea\u52a8\u5316\u4efb\u52a1\u8c03\u5ea6\u4e0e\u8ba1\u7b97\u8d44\u6e90\u5206\u914d\uff0c\u652f\u6301\u5728\u9ad8\u6027\u80fd\u8ba1\u7b97\u96c6\u7fa4\u4e0a\u5bf9\u5927\u6279\u91cf\u914d\u4f53\u5206\u5b50\u5e76\u884c\u8ba1\u7b97\uff0c\u80fd\u591f\u5927\u5e45\u63d0\u5347\u8ba1\u7b97\u6548\u7387\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><img fetchpriority=\"high\" decoding=\"async\" class=\"alignnone wp-image-346\" src=\"http:\/\/drtem.cn\/wp-content\/uploads\/2025\/03\/\u56fe\u72471.png\" alt=\"\" width=\"538\" height=\"227\" srcset=\"https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u56fe\u72471.png 1639w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u56fe\u72471-300x127.png 300w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u56fe\u72471-768x324.png 768w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u56fe\u72471-1536x649.png 1536w\" sizes=\"(max-width: 538px) 100vw, 538px\" \/><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\ud83d\ude80\u00a0<strong><b>\u6838\u5fc3\u4f18\u52bf<\/b><\/strong><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u2705\u00a0<strong><b>\u81ea\u52a8\u5316\u6d41\u7a0b<\/b><\/strong>\uff1a\u5305\u542b<strong><b>\u4f53\u7cfb\u6784\u5efa\u3001<\/b><\/strong><strong><b>\u5206\u5b50\u52a8\u529b\u5b66\u5e73\u8861\u3001<\/b><\/strong><strong><b>\u81ea\u7531\u80fd\u8ba1\u7b97<\/b><\/strong><strong><b>\u53ca\u7ed3\u679c\u5206\u6790<\/b><\/strong>\u7684\u5b8c\u6574\u6d41\u7a0b\uff0c\u6781\u5927\u51cf\u5c11\u7528\u6237\u5e72\u9884\uff0c\u5b9e\u73b0\u8f83\u9ad8\u7a0b\u5ea6\u7684\u81ea\u52a8\u5316\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u2705\u00a0<strong><b>\u9ad8\u7cbe\u5ea6\u9884\u6d4b<\/b><\/strong>\uff1a\u57fa\u4e8e<strong><b>\u4e25\u683c\u7684<\/b><\/strong><strong><b>\u70ed\u529b\u5b66\u5faa\u73af<\/b><\/strong>\uff0c\u4ee5AMBER\u8f6f\u4ef6\u4f5c\u4e3a\u5e95\u5c42\u5206\u5b50\u52a8\u529b\u5b66\u6a21\u62df\u5f15\u64ce\uff0c\u63d0\u4f9b\u53ef\u9760\u7684\u7ed3\u5408\u81ea\u7531\u80fd\u8ba1\u7b97\u7ed3\u679c\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u2705\u00a0<strong><b>\u9ad8\u6548\u7387<\/b><\/strong><strong><b>\u6279\u91cf\u8ba1\u7b97<\/b><\/strong>\uff1a\u652f\u6301SLURM\u8ba1\u7b97\u8d44\u6e90\u7ba1\u7406\u7cfb\u7edf\uff0c\u5b9e\u73b0\u5728\u9ad8\u6027\u80fd\u8ba1\u7b97\u96c6\u7fa4\u4e0a<strong><b>\u540c\u65f6\u8fd0\u884c\u5927\u6279\u91cf<\/b><\/strong><strong><b>\u914d\u4f53<\/b><\/strong><strong><b>\u7684\u8ba1\u7b97\u4efb\u52a1<\/b><\/strong>\uff0c\u5e76\u884c\u5904\u7406\u8f83\u5927\u89c4\u6a21\u836f\u7269\u7b5b\u9009\u4efb\u52a1\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u2705\u00a0<strong><b>\u5f00\u6e90\u53ef\u62d3\u5c55<\/b><\/strong>\uff1a\u7528Python\u5f00\u53d1\uff0c\u4ee3\u7801\u5f00\u6e90\uff0c<strong><b>\u652f\u6301\u7528\u6237\u6839\u636e\u5177\u4f53\u7814\u7a76<\/b><\/strong><strong><b>\u9700\u6c42\u8fdb\u884c\u4f18\u5316\u548c\u5b9a\u5236<\/b><\/strong>\uff0c\u7075\u6d3b\u9002\u5e94\u4e0d\u540c\u8ba1\u7b97\u573a\u666f\u4e0b\u7684\u79d1\u5b66\u95ee\u9898\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\ud83d\udccc<strong><b>\u6280\u672f\u5185\u6838\uff1aABFE\u70ed\u529b\u5b66\u5faa\u73af\uff1a<\/b><\/strong><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><strong><b>\u901a\u8fc7\u4e00\u7cfb\u5217\u70ed\u529b\u5b66\u53d8\u6362\uff0c<\/b><\/strong><strong><b>\u5c06<\/b><\/strong><strong><b>\u914d\u4f53\u5206\u5b50<\/b><\/strong><strong><b>\u4ece\u6c34\u76f8\u4e2d\u7684<\/b><\/strong><strong><b>\u81ea\u7531<\/b><\/strong><strong><b>\u72b6\u6001\u8f6c\u53d8\u4e3a\u4e0e\u86cb\u767d\u8d28\u9776\u6807\u7ed3\u5408\u7684\u590d\u5408\u7269<\/b><\/strong><strong><b>\uff0c\u7d2f\u52a0\u8fc7\u7a0b\u4e2d\u7684\u81ea\u7531\u80fd\u53d8\u83b7\u5f97\u8be5\u5c0f\u5206\u5b50\u4e0e\u9776\u6807\u86cb\u767d\u7684\u7edd\u5bf9\u7ed3\u5408\u81ea\u7531\u80fd\u0394G<\/b><\/strong><strong><sub><b>bind\u3002<\/b><\/sub><\/strong><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><img decoding=\"async\" class=\"alignnone wp-image-347\" src=\"http:\/\/drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466902292730.png\" alt=\"\" width=\"503\" height=\"284\" srcset=\"https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466902292730.png 554w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466902292730-300x169.png 300w\" sizes=\"(max-width: 503px) 100vw, 503px\" \/><\/span><\/p>\n<ol>\n<li><span style=\"color: #5e5e5e;\">\u0394G<sub>int,sol<\/sub>\u2192 \u5728\u6eb6\u6db2\u4e2d\u914d\u4f53\u7684\u53bb\u8026\u5408\uff08Decoupling in Solution\uff09<\/span>\n<ul>\n<li><span style=\"color: #5e5e5e;\">\u5173\u95ed\u914d\u4f53\u5728\u6c34\u6eb6\u6db2\u4e2d\u7684\u8303\u5fb7\u534e\u529b\u548c\u9759\u7535\u76f8\u4e92\u4f5c\u7528\uff0c\u4f7f\u5176\u4ece\u6eb6\u6db2\u201c\u6d88\u5931\u201d\u53d8\u6210\u7406\u60f3\u6c14\u4f53\u72b6\u6001\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\">\u8ba1\u7b97\u6a21\u62df\u8fd9\u4e00\u53bb\u8026\u5408\u8fc7\u7a0b\u4e2d\u81ea\u7531\u80fd\u7684\u53d8\u5316\u3002<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"color: #5e5e5e;\">\u0394G<sub>restr,dum<\/sub>\u2192 \u5bf9\u5c0f\u5206\u5b50\u4e0e\u86cb\u767d\u7684\u76f8\u5bf9\u4f4d\u7f6e\u65bd\u52a0\u7ea6\u675f\uff08Turning on\u00a0Restraints\uff09<\/span>\n<ul>\n<li><span style=\"color: #5e5e5e;\">\u5728\u53bb\u8026\u5408\u7684\u72b6\u6001\u4e0b\uff0c\u5bf9\u914d\u4f53\u65bd\u52a0Boresch \u7ea6\u675f\uff0c\u56fa\u5b9a\u5176\u5728\u7ed3\u5408\u4f4d\u70b9\u7684\u7a7a\u95f4\u4f4d\u7f6e\u548c\u53d6\u5411\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\">\u8fd9\u90e8\u5206\u7684\u81ea\u7531\u80fd\u53d8\u5316\u53ef\u4ee5\u901a\u8fc7\u89e3\u6790\u8ba1\u7b97\u83b7\u5f97\uff0c\u65e0\u9700\u989d\u5916\u6a21\u62df\u3002<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"color: #5e5e5e;\">\u0394G<sub>int,com<\/sub>\u2192 \u5728\u9776\u86cb\u767d\u7684\u7ed3\u5408\u53e3\u888b\u4e2d\u914d\u4f53\u7684\u91cd\u8026\u5408\uff08Recoupling in Binding Site\uff09<\/span>\n<ul>\n<li><span style=\"color: #5e5e5e;\">\u8ba9\u914d\u4f53\u5728\u86cb\u767d\u7ed3\u5408\u4f4d\u70b9\u91cd\u65b0\u6062\u590d\u8303\u5fb7\u534e\u548c\u9759\u7535\u76f8\u4e92\u4f5c\u7528\uff0c\u6a21\u62df\u5176\u4ece\u65e0\u76f8\u4e92\u4f5c\u7528\u72b6\u6001\u53d8\u4e3a\u5b8c\u5168\u7ed3\u5408\u72b6\u6001\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\">\u8ba1\u7b97\u6a21\u62df\u8fd9\u4e00\u8026\u5408\u8fc7\u7a0b\u4e2d\u81ea\u7531\u80fd\u7684\u53d8\u5316\u3002<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"color: #5e5e5e;\">\u0394G<sub>restr,com<\/sub>\u2192 \u53bb\u9664\u7ea6\u675f\u529b\uff08Turning off\u00a0Restraints\uff09<\/span>\n<ul>\n<li><span style=\"color: #5e5e5e;\">\u89e3\u9664Boresch \u7ea6\u675f\uff0c\u5141\u8bb8\u914d\u4f53\u80fd\u591f\u5728\u7ed3\u5408\u4f4d\u70b9\u81ea\u7531\u8fd0\u52a8\uff0c\u6062\u590d\u5176\u771f\u5b9e\u72b6\u6001\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\">\u8ba1\u7b97\u6a21\u62df\u53bb\u9664\u7ea6\u675f\u529b\u8fc7\u7a0b\u7684\u81ea\u7531\u80fd\u53d8\u5316\u3002<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<p><span style=\"color: #5e5e5e;\">\u901a\u8fc7\u4e0a\u8ff0\u56db\u6b65\u8ba1\u7b97\u51fa\u4f53\u7cfb\u4e2d\u4e0d\u540c\u76f8\u4e92\u4f5c\u7528\u7684\u81ea\u7531\u80fd\u53d8\u5316\uff0c\u6700\u7ec8\u4ee5\u83b7\u5f97\u7edd\u5bf9\u7ed3\u5408\u81ea\u7531\u80fd\uff0c\u7528\u4e8e\u8bc4\u4f30\u914d\u4f53\u548c\u86cb\u767d\u7684\u7ed3\u5408\u5f3a\u5ea6\u3002<\/span><\/p>\n<ul>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>\u8ba1\u7b97\u6d41\u7a0b\uff1a<\/b><\/strong><\/span><\/li>\n<\/ul>\n<ol>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Topology Construction<\/b><\/strong>\uff1a\u751f\u6210\u6a21\u62df\u6240\u9700\u7684\u62d3\u6251\u6587\u4ef6\u53ca\u529b\u573a\u53c2\u6570\uff0c\u5305\u62ec\u53c2\u6570\u5316\u914d\u4f53\u3001\u86cb\u767d\u8d28\u3001\u6c34\u6eb6\u6db2\u53ca\u79bb\u5b50\u7b49\u7ec4\u5206\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Equilibration Simulation<\/b><\/strong>\uff1a\u901a\u8fc7\u4e00\u7cfb\u5217\u5206\u5b50\u52a8\u529b\u5b66\u6a21\u62df\u6b65\u9aa4\u4f7f\u4f53\u7cfb\u9010\u6b65\u8fbe\u5230\u70ed\u529b\u5b66\u5e73\u8861\u3002\u8fd9\u4e9b\u6b65\u9aa4\u5305\u62ec\u80fd\u91cf\u6700\u5c0f\u5316\u3001\u5206\u9636\u6bb5\u5347\u6e29\u4ee5\u53ca\u6052\u538b\u6052\u6e29\uff08NPT\uff09\u6a21\u62df\uff0c\u786e\u4fdd\u540e\u7eed\u81ea\u7531\u80fd\u8ba1\u7b97\u7684\u53ef\u9760\u6027\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Alchemy Morph<\/b><\/strong>\uff1a\u6839\u636e\u81ea\u7531\u80fd\u8ba1\u7b97\u8def\u5f84\u8bbe\u8ba1\u914d\u4f53\u5728\u4e0d\u540c\u7269\u7406\u72b6\u6001\u4e4b\u95f4\u7684\u53d8\u6362\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Alchemy Simulation<\/b><\/strong>\uff1a\u5728\u4e00\u7cfb\u5217\u9884\u5b9a\u4e49\u7684\u03bb \u72b6\u6001\u4e0b\u6267\u884c\u70bc\u91d1\u672f\u6a21\u62df\uff0c\u8ba1\u7b97\u4e0d\u540c\u72b6\u6001\u95f4\u7684\u81ea\u7531\u80fd\u53d8\u5316\u3002\u901a\u8fc7\u9010\u6b65\u8c03\u6574\u5206\u5b50\u95f4\u76f8\u4e92\u4f5c\u7528\uff0c\u5e73\u6ed1\u6574\u4e2a\u72b6\u6001\u8dc3\u8fc1\u8fc7\u7a0b\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Alchemy Analysis<\/b><\/strong>\uff1a\u57fa\u4e8e\u70bc\u91d1\u672f\u6a21\u62df\u751f\u6210\u7684\u91c7\u6837\u6570\u636e\uff0c\u5229\u7528\u7edf\u8ba1\u529b\u5b66\u65b9\u6cd5\uff08MBAR\u3001TI \uff09\u8ba1\u7b97\u81ea\u7531\u80fd\u53d8\u5316\uff08\u2206G\uff09\u3002\u540c\u65f6\u901a\u8fc7\u8bc4\u4f30\u8bef\u5dee\u548c\u6536\u655b\u6027\uff0c\u9a8c\u8bc1\u8ba1\u7b97\u7ed3\u679c\u7684\u51c6\u786e\u6027\u3002<\/span><\/li>\n<\/ol>\n<ul>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>\u8ba1\u7b97\u53c2\u8003\u793a\u4f8b\uff1a<\/b><\/strong><\/span><\/li>\n<\/ul>\n<p><span style=\"color: #5e5e5e;\">\ud83d\udd17GitHub\uff1a<strong><em><u><b><i>(<\/i><\/b><\/u><\/em><\/strong><a style=\"color: #5e5e5e;\" href=\"https:\/\/github.com\/freeenergylab\/FEP-SPell-ABFE\/tree\/main\/testing\"><strong><em><u><b><i>https:\/\/github.com\/freeenergylab\/FEP-SPell-ABFE\/tree\/main\/testing<\/i><\/b><\/u><\/em><\/strong><\/a><strong><em><u><b><i>)<\/i><\/b><\/u><\/em><\/strong><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u6b64\u6d4b\u8bd5\u5bf9\u5e94\u4e3a\u5de5\u4f5c\u6d41\u7684\u7528\u6cd5\u793a\u4f8b\u3002\u672c\u4f8b\u4e2d\u5c06\u4f1a\u5bf9\u4e0e\u53d7\u4f53\u86cb\u767d181L\u7ed3\u5408\u7684\u82ef\u548c\u82ef\u915a\u4e24\u4e2a\u914d\u4f53\u5206\u5b50\u5206\u522b\u8fdb\u884cABFE\u8ba1\u7b97\u3002\u6587\u4ef6\u5939\u7ed3\u6784\u5982\u4e0b\uff1a<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><img decoding=\"async\" class=\"alignnone wp-image-348 size-full\" src=\"http:\/\/drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466902844432.png\" alt=\"\" width=\"378\" height=\"359\" srcset=\"https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466902844432.png 378w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466902844432-300x285.png 300w\" sizes=\"(max-width: 378px) 100vw, 378px\" \/><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u7528\u6237\u53ef\u4ee5\u5c06\u6b64\u76ee\u5f55\u590d\u5236\u5230\u65b0\u7684\u5de5\u4f5c\u76ee\u5f55\u4e0b\uff0c\u540c\u65f6\u6839\u636e\u5f53\u524d\u8f6f\u4ef6\u5305\u8bbe\u7f6e\u76f8\u5173\u73af\u5883\u53d8\u91cf\u4ee5\u9002\u5e94\u8ba1\u7b97\u73af\u5883\uff08\u53c2\u8003submitBFE.sh\u6587\u4ef6\u4e2d\u7684\u8bbe\u7f6e\u7528\u6237\u5b9a\u4e49\u53d8\u91cf\u90e8\u5206\uff09\uff0c\u5e76\u4e14\u5728config.yaml\u6587\u4ef6\u4e2d\u4fee\u6539slurm\u63a7\u5236\u53c2\u6570\uff0c\u76f8\u5173\u5185\u5bb9\u53ef\u4ee5\u8fdb\u4e00\u6b65\u53c2\u8003GitHub\u4e2dREADME.md\u6587\u4ef6\u8fdb\u884c\u4fee\u6539\u9002\u914d\u3002\u63d0\u4ea4\u4f5c\u4e1a\u76f8\u5173\u547d\u4ee4\u5982\u4e0b\uff1a<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-349 size-full\" src=\"http:\/\/drtem.cn\/wp-content\/uploads\/2025\/03\/1746690305642.png\" alt=\"\" width=\"554\" height=\"78\" srcset=\"https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/1746690305642.png 554w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/1746690305642-300x42.png 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" \/><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u5f53\u6240\u6709\u6a21\u5757\u7684\u4efb\u52a1\u6210\u529f\u7ed3\u675f\uff0c\u5c31\u4f1a\u5728\u5de5\u4f5c\u76ee\u5f55\u4e2d\u751f\u6210\u51e0\u4e2a\u4e2d\u95f4\u6587\u4ef6\u5939\uff08\u4ee5\u4e0b\u5212\u7ebf \u201c_\u201d\u5f00\u5934\uff09\u548c\u6700\u7ec8\u7ed3\u679c\u6587\u4ef6dG_results.csv\u548cdG_components_results.csv\u3002dG_results.csv\u6587\u4ef6\u4e3a\u9884\u6d4b\u914d\u4f53\u7684\u7edd\u5bf9\u7ed3\u5408\u81ea\u7531\u80fd\u6570\u503c\uff0cdG_components_results.csv\u5217\u51fa\u4e86\u6bcf\u4e2a\u914d\u4f53\u5206\u5b50\u5728\u5404\u4e2a\u70ed\u529b\u5b66\u53d8\u6362\u6b65\u9aa4\u4e2d\u7684\u81ea\u7531\u80fd\u53d8\u5316\u503c\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\ud83d\udcca\u00a0<strong><b>\u9a8c\u8bc1\u7ed3\u679c\uff1a\u9ad8\u7cbe\u5ea6\u81ea\u7531\u80fd\u8ba1\u7b97<\/b><\/strong><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">FEP-SPell-ABFE \u5df2\u5728\u591a\u4e2a\u86cb\u767d-\u914d\u4f53\u4f53\u7cfb\u4e0a\u8fdb\u884c\u4e86\u57fa\u51c6\u6d4b\u8bd5\uff0c\u5e76\u4e0e\u5b9e\u9a8c\u6570\u636e\u5bf9\u6bd4\uff0c\u8868\u73b0\u51fa\u6781\u9ad8\u7684\u9884\u6d4b\u51c6\u786e\u6027\u3002<\/span><\/p>\n<p><span style=\"color: #5e5e5e;\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-350 size-full\" src=\"http:\/\/drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466903284267.png\" alt=\"\" width=\"321\" height=\"302\" srcset=\"https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466903284267.png 321w, https:\/\/www.drtem.cn\/wp-content\/uploads\/2025\/03\/\u4f01\u4e1a\u5fae\u4fe1\u622a\u56fe_17466903284267-300x282.png 300w\" sizes=\"(max-width: 321px) 100vw, 321px\" \/><\/span><\/p>\n<p><span style=\"color: #5e5e5e;\">\u6570\u636e\u8868\u660e\uff0c<strong><b>FEP-SPell-ABFE \u8ba1\u7b97\u51fa\u7684\u7ed3\u5408\u81ea\u7531\u80fd\u4e0e\u5b9e\u9a8c\u6d4b\u91cf\u6570\u636e\u9ad8\u5ea6\u4e00\u81f4<\/b><\/strong>\uff0c\u5177\u6709\u8f83\u5f3a\u7684\u9884\u6d4b\u7cbe\u5ea6\uff0c\u8868\u660e\u5176\u5728\u836f\u7269\u7b5b\u9009\u4e2d\u7684\u5e94\u7528\u6f5c\u529b\uff1a<\/span><\/p>\n<ul>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>L99A<\/b><\/strong><strong><b>\uff08\u4e2d\u6027\u914d\u4f53\u5206\u5b50\uff09<\/b><\/strong><strong><b>\uff1a<\/b><\/strong>RMSE 27\u00a0kcal\/mol\uff0cPearson \u76f8\u5173\u7cfb\u6570 1.00\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>BRD4<\/b><\/strong><strong><b>\uff08\u4e2d\u6027\u914d\u4f53\u5206\u5b50\uff09<\/b><\/strong><strong><b>\uff1a<\/b><\/strong>RMSE 1.81 kcal\/mol\uff0cPearson \u76f8\u5173\u7cfb\u6570 0.71\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>TYK2<\/b><\/strong><strong><b>\uff08\u4e2d\u6027\u914d\u4f53\u5206\u5b50\uff09<\/b><\/strong><strong><b>\uff1a<\/b><\/strong>RMSE 0.99 kcal\/mol\uff0cPearson \u76f8\u5173\u7cfb\u6570 0.78\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Thrombin\uff08+1\u4ef7\u914d\u4f53\u5206\u5b50\uff09\uff1a<\/b><\/strong>RMSE 1.04 kcal\/mol\uff0cPearson \u76f8\u5173\u7cfb\u6570 0.53\u3002<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>\u5f00\u6e90\u5171\u4eab<\/b><\/strong><\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>GitHub<\/b><\/strong><strong><b>\uff1a <\/b><\/strong><a style=\"color: #5e5e5e;\" href=\"https:\/\/github.com\/freeenergylab\/FEP-SPell-ABFE\"><strong><u><b>https:\/\/github.com\/freeenergylab\/FEP-SPell-ABFE<\/b><\/u><\/strong><\/a>\uff0c\u91c7\u7528 MIT \u8bb8\u53ef\uff0c\u514d\u8d39\u4f7f\u7528<\/span><\/li>\n<li><span style=\"color: #5e5e5e;\"><b><\/b><strong><b>Benchmark\uff1a<\/b><\/strong><a style=\"color: #5e5e5e;\" href=\"https:\/\/github.com\/freeenergylab\/FEP-SPell-ABFE-benchmark\"><strong><u><b>https:\/\/github.com\/freeenergylab\/FEP-SPell-ABFE-benchmark<\/b><\/u><\/strong><\/a><\/span><\/li>\n<\/ul>","protected":false},"excerpt":{"rendered":"<p>\u52a0\u5165\u884c\u4e1a\u9886\u8896\uff0c\u53c2\u52a0\u4e9a\u6d32\u6700\u5927\u7684\u4ece\u9972\u6599\u5230\u98df\u54c1\u7684\u6d3b\u52a8\u3002\u8be5\u6d3b\u52a8\u4e13\u6ce8\u4e8e\u755c\u7267\u4e1a\u751f\u4ea7\u3001\u52a8\u7269\u86cb\u767d\u751f\u4ea7\u4ee5\u53ca\u6240\u6709\u76f8\u5173\u9886\u57df\uff0c\u5982\u9972\u6599\u751f\u4ea7\u3001\u52a8\u7269\u517b\u6b96\u3001\u8089\u7c7b\u3001\u9c7c\u7c7b\u3001\u867e\u7c7b\u3001\u86cb\u7c7b\u3001\u4e73\u5236\u54c1\u7b49\u7684\u52a0\u5de5\u3002\u53d1\u73b0\u65b0\u673a\u4f1a\uff0c\u4e0e\u5173\u952e\u53c2\u4e0e\u8005\u5efa\u7acb\u8054\u7cfb\uff0c\u5728\u4e0d\u65ad\u53d1\u5c55\u53d8\u5316\u7684\u5168\u7403\u98df\u54c1\u8d38\u6613\u683c\u5c40\u4e2d\u4fdd\u6301\u9886\u5148\u5730\u4f4d\u3002<\/p>","protected":false},"author":1,"featured_media":346,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[7],"tags":[],"class_list":["post-113","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-local"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/posts\/113","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/comments?post=113"}],"version-history":[{"count":2,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/posts\/113\/revisions"}],"predecessor-version":[{"id":875,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/posts\/113\/revisions\/875"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/media\/346"}],"wp:attachment":[{"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/media?parent=113"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/categories?post=113"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.drtem.cn\/en\/wp-json\/wp\/v2\/tags?post=113"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}