{"id":60954,"date":"2024-10-11T10:30:08","date_gmt":"2024-10-11T02:30:08","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60954"},"modified":"2024-10-11T10:30:08","modified_gmt":"2024-10-11T02:30:08","slug":"%e4%b8%8d%e6%87%82%e4%bb%a3%e7%a0%81%e4%b9%9f%e5%88%ab%e6%80%95%ef%bc%81bio3d%e5%8c%85%ef%bc%8c%e8%ae%a9%e4%bd%a0%e8%bd%bb%e6%9d%be%e8%a7%a3%e6%9e%90%e8%9b%8b%e7%99%bd%e8%b4%a8%e4%b8%89%e7%bb%b4","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60954","title":{"rendered":"\u4e0d\u61c2\u4ee3\u7801\u4e5f\u522b\u6015\uff01Bio3D\u5305\uff0c\u8ba9\u4f60\u8f7b\u677e\u89e3\u6790\u86cb\u767d\u8d28\u4e09\u7ef4\u7ed3\u6784\uff0c\u52a9\u4f60\u5feb\u901f\u5165\u95e8\u751f\u4fe1\u5206\u6790\uff01"},"content":{"rendered":"\n
\"\"<\/figure>\n\n\n\n

\u5927\u5bb6\u597d\uff01\u4eca\u5929\u5c0f\u5e08\u59b9\u8981\u5411\u5927\u5bb6\u4ecb\u7ecd\u4e00\u4e2a\u5728\u7ed3\u6784\u751f\u7269\u4fe1\u606f\u5b66\u9886\u57df\u4e2d\u975e\u5e38\u91cd\u8981\u7684R\u5305\u2014\u2014Bio3D\u5305\uff01Bio3D\u5305\u662f\u4e13\u95e8\u7528\u4e8e\u5206\u6790\u751f\u7269\u5927\u5206\u5b50\u4e09\u7ef4\u7ed3\u6784\u7684\u5f3a\u5927\u5de5\u5177\u3002\u968f\u7740\u7ed3\u6784\u751f\u7269\u5b66\u7684\u53d1\u5c55\uff0c\u8d8a\u6765\u8d8a\u591a\u7684\u751f\u7269\u5927\u5206\u5b50\u7ed3\u6784\u6570\u636e\u88ab\u89e3\u5bc6\u548c\u5e94\u7528\uff0cBio3D\u5305\u80fd\u591f\u5e2e\u52a9\u6211\u4eec\u6df1\u5165\u5206\u6790\u8fd9\u4e9b\u7ed3\u6784\u6570\u636e\uff0c\u5e76\u901a\u8fc7\u591a\u79cd\u7b97\u6cd5\u63ed\u793a\u751f\u7269\u5206\u5b50\u4e4b\u95f4\u7684\u52a8\u6001\u5173\u7cfb\u3002\u5b83\u53ef\u4ee5\u5904\u7406\u86cb\u767d\u8d28\u7684\u4e09\u7ef4\u7ed3\u6784\uff0c\u6267\u884c\u5305\u62ec\u7ed3\u6784\u6bd4\u5bf9\u3001\u5206\u5b50\u52a8\u529b\u5b66\u8f68\u8ff9\u5206\u6790\u3001\u6b63\u89c4\u6a21\u5f0f\u5206\u6790\uff08NMA\uff09\u7b49\u4efb\u52a1\uff0c\u5bf9\u7814\u7a76\u86cb\u767d\u8d28\u7684\u7ed3\u6784\u529f\u80fd\u5173\u7cfb\u6709\u91cd\u8981\u5e2e\u52a9\u3002\u5c0f\u5e08\u59b9\u53ef\u662f\u5389\u5bb3\u7684\u751f\u4fe1\u9ad8\u624b\uff0c\u8981\u662f\u540c\u5b66\u4eec\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u86cb\u767d\u8d28\u7ed3\u6784\u5206\u6790\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u6211\uff01\uff01<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u672c\u6b21\u5b66\u4e60\u4e2d\uff0c\u6211\u4eec\u4e0d\u4ec5\u5c06\u5b66\u4f1a\u5982\u4f55\u5b89\u88c5\u548c\u4f7f\u7528Bio3D\u5305\uff0c\u8fd8\u5c06\u638c\u63e1\u5982\u4f55\u63d0\u53d6\u86cb\u767d\u8d28\u7684\u4e09\u7ef4\u7ed3\u6784\u6570\u636e\u3001\u6267\u884c\u6b63\u89c4\u6a21\u5f0f\u5206\u6790\u3001\u5e76\u7ed3\u5408\u4e8c\u7ea7\u7ed3\u6784\u4fe1\u606f\u5c55\u793a\u67d4\u6027\u7279\u5f81\u7684\u53ef\u89c6\u5316\u65b9\u6cd5\u3002\u901a\u8fc7\u5b9e\u9645\u793a\u4f8b\u7684\u6f14\u793a\uff0c\u6211\u4eec\u5c06\u6df1\u5165\u4e86\u89e3Bio3D\u5305\u7684\u529f\u80fd\uff0c\u4e3a\u7814\u7a76\u751f\u7269\u5206\u5b50\u7ed3\u6784\u4e0e\u529f\u80fd\u7684\u5173\u7cfb\u63d0\u4f9b\u5b9d\u8d35\u5de5\u5177\u3002\u6211\u76f8\u4fe1\uff0c\u901a\u8fc7\u4eca\u5929\u7684\u5b66\u4e60\uff0c\u540c\u5b66\u4eec\u90fd\u80fd\u591f\u66f4\u52a0\u719f\u7ec3\u5730\u5e94\u7528Bio3D\u5305\uff0c\u4e3a\u7ed3\u6784\u751f\u7269\u4fe1\u606f\u5b66\u7684\u7814\u7a76\u8fdb\u6b65\u8d21\u732e\u81ea\u5df1\u7684\u4e00\u4efd\u529b\u91cf\uff01\u63a5\u4e0b\u6765\uff0c\u540c\u5b66\u4eec\u8ddf\u7d27\u5c0f\u5e08\u59b9\u7684\u6b65\u4f10\uff0c\u8ba9\u6211\u4eec\u6b63\u5f0f\u5f00\u542f\u5bf9Bio3D\u5305\u7684\u5b66\u4e60\u4e4b\u65c5\u5427\uff01<\/p>\n\n\n\n

\u672c\u6b21\u4ecb\u7ecd\u7684R\u5305\u5728\u670d\u52a1\u5668\u4e0a\u80fd\u66f4\u52a0\u6d41\u7545\u5730\u8fd0\u884c\uff0c\u5982\u679c\u6ca1\u6709\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u8054\u7cfb\u6211\u4eec\u8fdb\u884c\u670d\u52a1\u5668\u79df\u8d41~<\/strong><\/strong><\/p>\n\n\n\n

Bio3D\u5305\u4ecb\u7ecd<\/p>\n\n\n\n

Bio3D\u662f\u4e00\u4e2a\u7528\u4e8e\u7ed3\u6784\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684R\u8bed\u8a00\u5305\uff0c\u4e3b\u8981\u7528\u4e8e\u751f\u7269\u5927\u5206\u5b50\uff08\u5982\u86cb\u767d\u8d28\u548c\u6838\u9178\uff09\u4e09\u7ef4\u7ed3\u6784\u6570\u636e\u7684\u5904\u7406\u548c\u5206\u6790\u3002\u5b83\u80fd\u591f\u6267\u884c\u5404\u79cd\u7ed3\u6784\u5206\u6790\u4efb\u52a1\uff0c\u5982\u7ed3\u6784\u5bf9\u63a5\u3001\u540c\u6e90\u5efa\u6a21\u3001\u5206\u5b50\u52a8\u529b\u5b66\u6a21\u62df\u8f68\u8ff9\u5206\u6790\u3001\u7ed3\u6784\u6bd4\u5bf9\u7b49\u3002Bio3D\u7684\u6838\u5fc3\u529f\u80fd\u5305\u62ec\u4ecePDB\u6570\u636e\u5e93\u4e2d\u63d0\u53d6\u7ed3\u6784\u6570\u636e\u3001\u8ba1\u7b97\u7ed3\u6784\u76f8\u4f3c\u6027\u3001\u751f\u6210\u7ed3\u6784\u6bd4\u5bf9\u548c\u805a\u7c7b\u5206\u6790\uff0c\u4ee5\u53ca\u5206\u6790\u86cb\u767d\u8d28\u52a8\u529b\u5b66\u7279\u5f81\uff0c\u5982\u4e3b\u6210\u5206\u5206\u6790\uff08PCA\uff09\u548c\u6b63\u89c4\u6a21\u5f0f\u5206\u6790\uff08NMA\uff09\u3002\u8be5\u5305\u5e7f\u6cdb\u5e94\u7528\u4e8e\u86cb\u767d\u8d28\u529f\u80fd\u7814\u7a76\u3001\u5206\u5b50\u6f14\u5316\u7814\u7a76\u4ee5\u53ca\u836f\u7269\u8bbe\u8ba1\u7b49\u9886\u57df\uff0c\u5e2e\u52a9\u7814\u7a76\u8005\u6df1\u5165\u7406\u89e3\u751f\u7269\u5206\u5b50\u7ed3\u6784\u4e0e\u529f\u80fd\u7684\u5173\u7cfb\u3002<\/p>\n\n\n\n

Bio3D\u5305\u5b89\u88c5<\/p>\n\n\n\n

\u9700\u8981R\u8bed\u8a00\u7248\u672c\u4e3a4.4\uff0c\u5728\u63a7\u5236\u53f0\u4e2d\u8f93\u5165\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n\n\n\n

install.packages(“bio3d”, dependencies=TRUE)<\/p>\n\n\n\n

\u67e5\u770b\u662f\u5426\u5b89\u88c5\u6210\u529f\uff1a<\/p>\n\n\n\n

packageVersion(“Bio3D”) # \u67e5\u770bBio3D\u7248\u672c<\/p>\n\n\n\n

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

\u663e\u793a\u4e3a2.4.4\u7248\u672c\uff0c\u5219\u8868\u793a\u5df2\u7ecf\u5b89\u88c5\u4e86Bio3D\u5305\u3002<\/p>\n\n\n\n

\u901a\u8fc7Bio3D\u5305\u7684\u6b63\u89c4\u6a21\u5f0f\u5206\u6790\uff08NMA\uff09\u6765\u5206\u6790\u86cb\u767d\u8d28\u7684\u4e09\u7ef4\u7ed3\u6784<\/p>\n\n\n\n

\u8f7d\u5165\u9700\u8981\u7684\u5305\u548c\u6570\u636e<\/strong><\/strong><\/p>\n\n\n\n

\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u8f7d\u5165\u672c\u6b21\u5b66\u4e60\u7684\u4e3b\u89d2\u2014\u2014Bio3D\u5305\u3002<\/p>\n\n\n\n

library(bio3d) # \u8f7d\u5165bio3d\u5305<\/p>\n\n\n\n

\u5728\u672c\u6587\u4e2d\uff0c\u5c0f\u5e08\u59b9\u5c06\u4f7f\u7528pdb\u6570\u636e\u5e93\u4e2d\u7f16\u53f7\u4e3a \u201c1HEL\u201d \u7684\u6eb6\u83cc\u9176\uff08Lysozyme\uff09\u4f5c\u4e3a\u793a\u4f8b\u86cb\u767d\uff0c\u901a\u8fc7\u4f7f\u7528bio3d\u5305\u7684\u6b63\u89c4\u6a21\u5f0f\u5206\u6790\uff08NMA\uff09\u6765\u5206\u6790\u5176\u67d4\u6027\u53ca\u4e8c\u7ef4\u7ed3\u6784\u7279\u5f81\u3002<\/p>\n\n\n\n

\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528bio3d\u5305\u4e2d\u7684read.pdb()\u51fd\u6570\u4ecepdb\u6570\u636e\u5e93\u4e2d\u4e0b\u8f7d\u6eb6\u83cc\u9176\u7684PDB\u6587\u4ef6\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

pdb <- read.pdb(“1hel”) # \u4e0b\u8f7d\u6eb6\u83cc\u9176\u7684PDB\u6587\u4ef6<\/p>\n\n\n\n

print(pdb) # \u663e\u793a\u793a\u4f8b\u86cb\u767d\u57fa\u7840\u4fe1\u606f<\/p>\n\n\n\n

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

\u53ef\u77e5\u6eb6\u83cc\u9176\u662f\u7531129\u4e2a\u6c28\u57fa\u9178\u6b8b\u57fa\uff0c1186\u4e2a\u539f\u5b50\u7ec4\u6210\u7684\u5355\u94fe\u86cb\u767d\u8d28\u3002<\/p>\n\n\n\n

\u5982\u679c\u60f3\u8981\u8be6\u7ec6\u67e5\u770b\u539f\u5b50\u6784\u6210\u4ee5\u53ca\u5750\u6807\u4fe1\u606f\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u547d\u4ee4\uff1a<\/p>\n\n\n\n

head(pdb$atom) #\u67e5\u770b\u539f\u5b50\u4fe1\u606f<\/p>\n\n\n\n

print(pdb$xyz) #\u67e5\u770b\u539f\u5b50\u5750\u6807<\/p>\n\n\n\n

\u663e\u793a\u5982\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

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

\u8fdb\u884c\u86cb\u767d\u8d28\u4e09\u7ef4\u7ed3\u6784\u5206\u6790<\/strong><\/strong><\/p>\n\n\n\n

\u5728\u672c\u6587\u4e2d\uff0c\u6211\u4eec\u5c06\u4f7f\u7528bio3d\u5305\u4e2d\u7684nma\uff08\uff09\u51fd\u6570\uff0c\u8fdb\u884c\u6b63\u89c4\u6a21\u5f0f\u5206\u6790\uff08NMA\uff09\uff0c\u4ece\u800c\u9884\u6d4b\u793a\u4f8b\u86cb\u767d\u8d28\u7684\u67d4\u6027\u3002\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

modes <- nma(pdb) # \u4f7f\u7528bio3d\u5305\u8fdb\u884c\u8fdb\u884c\u86cb\u767d\u8d28\u4e09\u7ef4\u7ed3\u6784\u5206\u6790\u3002<\/p>\n\n\n\n

plot(modes) # \u4f7f\u7528plot\uff08\uff09\u51fd\u6570\u5c55\u793a\u5206\u6790\u7ed3\u679c\u3002<\/p>\n\n\n\n

\u663e\u793a\u7ed3\u679c\u5982\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

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

\u7531\u56fe\u53ef\u77e5\uff0c\u4e0a\u65b9\u4e24\u4e2a\u56fe\u5206\u522b\u663e\u793a\u4e86\u7279\u5f81\u503c\uff08Eigenvalues\uff09\u548c\u9891\u7387\uff08Frequencies\uff09\u968f\u6a21\u5f0f\u6307\u6570\uff08Mode Index\uff09\u7684\u53d8\u5316\u3002\u7279\u5f81\u503c\u4ece\u5de6\u81f3\u53f3\u9012\u589e\uff0c\u8bf4\u660e\u9ad8\u6a21\u5f0f\u5bf9\u5e94\u7684\u521a\u6027\u8f83\u5927\uff0c\u8fd0\u52a8\u8f83\u96be\u53d1\u751f\u3002\u9891\u7387\u56fe\u4e0e\u7279\u5f81\u503c\u5bc6\u5207\u76f8\u5173\uff0c\u4e5f\u8868\u73b0\u51fa\u9012\u589e\u8d8b\u52bf\uff0c\u9ad8\u9891\u6a21\u5f0f\u5bf9\u5e94\u5c40\u90e8\u632f\u52a8\uff0c\u4f4e\u9891\u6a21\u5f0f\u5219\u4e0e\u5168\u5c40\u8fd0\u52a8\u76f8\u5173\u3002\u4e0b\u65b9\u7684\u6ce2\u52a8\u56fe\uff08Fluctuations\uff09\u5c55\u793a\u4e86\u86cb\u767d\u8d28\u5404\u6b8b\u57fa\u7684\u632f\u5e45\u6ce2\u52a8\u60c5\u51b5\u3002\u67d0\u4e9b\u6b8b\u57fa\u533a\u57df\uff08\u5982\u7b2c50\u300170\u548c120\u9644\u8fd1\uff09\u663e\u793a\u51fa\u8f83\u5927\u7684\u6ce2\u52a8\uff0c\u610f\u5473\u7740\u8fd9\u4e9b\u533a\u57df\u66f4\u5177\u67d4\u6027\uff0c\u53ef\u80fd\u5728\u86cb\u767d\u8d28\u529f\u80fd\u4e2d\u8d77\u91cd\u8981\u4f5c\u7528\u3002<\/p>\n\n\n\n

\u4e3a\u4e86\u80fd\u591f\u6e05\u6670\u7684\u5c55\u793a\u86cb\u767d\u8d28\u7684\u67d4\u6027\u548c\u5176\u4e8c\u7ea7\u7ed3\u6784\u4e4b\u95f4\u7684\u5173\u7cfb\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528plot.bio3d()\u51fd\u6570\u4e2d\u7684\u53c2\u6570\u5728\u6ce2\u52a8\u56fe\uff08Fluctuations\uff09\u4e0a\u6dfb\u52a0\u4e8c\u7ea7\u7ed3\u6784\u4fe1\u606f\uff0c\u4ee3\u7801\u5982\u4e0b\uff1a<\/p>\n\n\n\n

plot.bio3d(<\/p>\n\n\n\n

  modes$fluctuations,   # \u6b63\u5e38\u6a21\u5f0f\u5206\u6790\uff08NMA\uff09\u4e2d\u6bcf\u4e2a\u6b8b\u57fa\u7684\u6ce2\u52a8\u6570\u636e<\/p>\n\n\n\n

  sse=pdb,              # \u63d0\u4f9bPDB\u5bf9\u8c61\u4ee5\u83b7\u53d6\u86cb\u767d\u8d28\u7684\u4e8c\u7ea7\u7ed3\u6784\u4fe1\u606f<\/p>\n\n\n\n

  sheet.col=”orange”,   # \u5c06\u03b2-\u6298\u53e0\u7684\u989c\u8272\u8bbe\u7f6e\u4e3a\u6a59\u8272\uff0c\u7528\u4e8e\u5728\u56fe\u4e2d\u533a\u5206\u4e8c\u7ea7\u7ed3\u6784<\/p>\n\n\n\n

  helix.col=”purple”,   # \u5c06\u03b1-\u87ba\u65cb\u7684\u989c\u8272\u8bbe\u7f6e\u4e3a\u7d2b\u8272\uff0c\u7528\u4e8e\u533a\u5206\u4e8c\u7ea7\u7ed3\u6784<\/p>\n\n\n\n

  typ=”l”,              # \u8bbe\u7f6e\u56fe\u5f62\u7c7b\u578b\u4e3a\u7ebf\u6761\u56fe\uff08line plot\uff09\uff0c\u5373\u7528\u7ebf\u8fde\u63a5\u6570\u636e\u70b9<\/p>\n\n\n\n

  lwd=3,                # \u5c06\u7ebf\u6761\u5bbd\u5ea6\u8bbe\u4e3a3\uff0c\u4f7f\u7ebf\u6761\u66f4\u52a0\u7c97\u58ee\uff0c\u56fe\u5f62\u66f4\u6e05\u6670<\/p>\n\n\n\n

  ylab=”Fluctuations from NMA (custom label)”  # \u8bbe\u7f6ey\u8f74\u6807\u7b7e\u4e3a\u81ea\u5b9a\u4e49\u5185\u5bb9<\/p>\n\n\n\n

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

\u7ed3\u679c\u663e\u793a\u5982\u4e0b\u56fe\uff1a<\/p>\n\n\n\n

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

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