PDB数据库简介 如何搜索PDB数据库？
PDB\u6570\u636e\u5e93\u7f51\u5740\u662f\u4ec0\u4e48\uff1fhttp://www.uniprot.org/
\u65b0\u7684\u201c\u8054\u5408\u86cb\u767d\u8d28\u6570\u636e\u5e93\u201d\u9884\u8ba1\u5728\u4e09\u5e74\u5185\u5efa\u6210\uff0c\u7f8e\u56fd\u56fd\u5bb6\u536b\u751f\u7814\u7a76\u6240\u5df2\u51b3\u5b9a\u4e3a\u8fd9\u9879\u8ba1\u5212\u65a5\u8d441500\u4e07\u7f8e\u5143\u3002\u8fd9\u4e00\u5168\u7403\u6027\u6570\u636e\u5e93\u6709\u671b\u57282003\u5e74\u5e74\u5e95\u521d\u6b65\u5728\u56e0\u7279\u7f51\u4e0a\u5f00\u653e\uff0c\u5404\u56fd\u7814\u7a76\u4eba
\u5458\u53ef\u901a\u8fc7\u8bbf\u95ee\u5176\u7f51\u5740www.uniprot.org\uff0c\u514d\u8d39\u83b7\u53d6\u4fe1\u606f\u3002(\u65b0\u6d6a\u7f51 2002\u5e7411\u670801\u65e5)
\u86cb\u767d\u8d28\u6570\u636e\u5e93\uff08Protein Data Bank, PDB\uff09\u662f\u4e00\u4e2a\u751f\u7269\u5927\u5206\u5b50\uff0c\u5982\u86cb\u767d\u8d28\u548c\u6838\u9178\uff0c\u7684\u6570\u636e\u5e93\u3002\u8fd9\u4e9b\u6570\u636e\u5305\u62ecX\u5149\u6676\u4f53\u884d\u5c04\u6216\u8005NMR\u6838\u78c1\u5171\u632f\u663e\u793a\u4ee5\u53ca\u7531\u5168\u4e16\u754c\u751f\u7269\u5b66\u5bb6\u548c\u751f\u7269\u5316\u5b66\u5bb6\u4e0a\u4f20\uff0c\u5728\u7f51\u4e0a\uff0c\u5b83\u4eec\u53ef\u4ee5\u901a\u8fc7PBD\u7684\u4f1a\u5458\u7ec4\u7ec7\uff08PDBe, PDBj, RCSB\uff09\u514d\u8d39\u83b7\u53d6\u3002PDB\u662f\u7531\u4e00\u4e2a\u53eb\u505a\u4e16\u754c\u86cb\u767d\u8d28\u6570\u636e\u5e93\uff08Worldwide Protein Data Bank, wwPDB\uff09\u7ba1\u7406\u3002PDB\u662f\u7ed3\u6784\u751f\u7269\uff08\u5982\u7ed3\u6784\u57fa\u56e0\u7ec4\u5b66\uff09\u7684\u4e00\u4e2a\u5173\u952e\u6027\u8d44\u6e90\u3002\u5927\u90e8\u5206\u5b66\u672f\u520a\u7269\uff0c\u4ee5\u53ca\u4e00\u4e9b\u5b98\u65b9\u79d1\u7814\u673a\u6784[\u5982\u7f8e\u56fd\u7684\u56fd\u7acb\u536b\u751f\u7814\u7a76\u9662\uff08NIH\uff09]\uff0c\u73b0\u5728\u90fd\u8981\u6c42\u79d1\u5b66\u5bb6\u5c06\u5b83\u4eec\u7814\u7a76\u7684\u86cb\u767d\u8d28\u3001\u6838\u9178\u7ed3\u6784\u4e0a\u4f20\u5230PDB
\u3000\u4ecePDB\u7684\u7f51\u7ad9\u4e0a\uff0c\u53ef\u4ee5\u901a\u8fc7\u86cb\u767d\u8d28\u7684\u7f16\u53f7\u67e5\u627e\u5230\u76f8\u5e94\u76843D\u7ed3\u6784\uff0c\u5e76\u53ef\u4ee5\u5c06\u8fd9\u4e2a\u7ed3\u6784\u56fe\u4e0b\u8f7d\u5230\u7535\u8111\u4e2d\uff0c\u901a\u8fc7PyMol\u3001RasMol\u3001Chimera\u3001VMD\u3001Swiss-PdbViewer\u7b49\u8f6f\u4ef6\u67e5\u770b\u3001\u7f16\u8f91\u3002 \u3000\u3000\u4ecePDB\u7f51\u7ad9\u4e0a\u4e0b\u8f7d\u76843D\u7ed3\u6784\u56fe\u7684\u540e\u7f00\u540d\u4e3a.pdb\u3002
PDB\u662fPalm DataBase\u7684\u7f29\u5199,Palm OS\u6240\u7528\u6587\u4ef6\u7684\u6269\u5c55\u540d\u4e3a.pdb\u3002\u53ef\u4ee5\u4f7f\u7528PalmReader\u6253\u5f00\u3002 \u5982\u679c\u60f3\u628aPDB\u6587\u4ef6\u8f6c\u6362\u6210TXT\u6587\u4ef6\u67e5\u770b\uff0c\u53ef\u4ee5\u4f7f\u7528WavePDB\u8f6c\u3002
\u3000\u3000\u7a0b\u5e8f\u6570\u636e\u5e93 (PDB) \u6587\u4ef6\u4fdd\u5b58\u7740\u8c03\u8bd5\u548c\u9879\u76ee\u72b6\u6001\u4fe1\u606f\uff0c\u4f7f\u7528\u8fd9\u4e9b\u4fe1\u606f\u53ef\u4ee5\u5bf9\u7a0b\u5e8f\u7684\u8c03\u8bd5\u914d\u7f6e\u8fdb\u884c\u589e\u91cf\u94fe\u63a5\u3002\u5e38\u89c1\u7684VC80.PDB\uff08\u66f4\u7b3c\u7edf\u5730\u8bf4\u5c31\u662f VCx0.PDB\uff0c\u5176\u4e2d x \u8868\u793a Visual C++ \u7684\u7248\u672c\u3002\uff09 \u8be5\u6587\u4ef6\u5b58\u50a8\u5404\u4e2a OBJ \u6587\u4ef6\u7684\u6240\u6709\u8c03\u8bd5\u4fe1\u606f\u5e76\u4e0e\u9879\u76ee\u751f\u6210\u6587\u4ef6\u9a7b\u7559\u5728\u540c\u4e00\u4e2a\u76ee\u5f55\u4e2d\u3002
绛旓細PDB鏁版嵁搴撶畝浠鐢熺墿鏁版嵁搴撶殑绉嶇被鐢熺墿鏁版嵁搴撶殑绉嶇被搴忓垪鏁版嵁搴•鏍搁吀搴忓垪鏁版嵁搴(EMBL銆丟enBank銆丏DBJ)•甯哥敤铔嬬櫧璐ㄥ簭鍒楁暟鎹簱(Swissprot,PIR)缁撴瀯鏁版嵁搴•铔嬬櫧璐ㄧ粨鏋勬暟鎹簱(PDB)•铔嬬櫧璐ㄥ垎绫绘暟鎹簱(SCOP銆丆ATH)鍏跺畠鏁版嵁搴揚roteinDataBank铔嬬櫧璐ㄧ粨鏋勬暟鎹簱http://www.rcsb.org/pdb/hom...
绛旓細PDB锛圥rotein Data Bank锛夋槸鍏ㄤ笘鐣屾渶澶х殑铔嬬櫧璐ㄧ粨鏋勬暟鎹簱銆傚畠鍖呭惈浜嗗ぇ閲忕殑铔嬬櫧璐ㄤ笁缁寸粨鏋勪俊鎭紝杩欎簺缁撴瀯淇℃伅鏄熀浜嶺灏勭嚎鏅朵綋瀛﹀拰鏍哥鍏辨尟绛夊疄楠屾墜娈靛緱鍒扮殑銆傜鐮斾汉鍛樺彲浠ラ氳繃璇ユ暟鎹簱鏌ヨ铔嬬櫧璐ㄧ殑缁撴瀯銆佸姛鑳戒互鍙婂叾浠栫浉鍏充俊鎭2. UniProt铔嬬櫧璐ㄦ暟鎹簱 UniProt鏄竴涓患鍚堟ц泲鐧借川鏁版嵁搴擄紝瀹冩彁渚涗簡铔嬬櫧璐ㄧ殑搴...
绛旓細PDB鏄敱涓栫晫铔嬬櫧璐ㄦ暟鎹簱锛圵orldwide Protein Data Bank,wwPDB锛夌鐞銆PDB鏄粨鏋勭敓鐗╁鐨勫叧閿ц祫婧锛屽ぇ閮ㄥ垎瀛︽湳鍒婄墿锛屼互鍙婁竴浜涘畼鏂圭鐮旀満鏋刐濡傜編鍥界殑鍥界珛鍗敓鐮旂┒闄紙NIH锛塢锛岀幇鍦ㄩ兘瑕佹眰绉戝瀹跺皢瀹冧滑鐮旂┒鐨勮泲鐧借川銆佹牳閰哥粨鏋勪笂浼犲埌PDB銆 浠嶱DB鐨勭綉绔欎笂锛屽彲浠ラ氳繃铔嬬櫧璐ㄧ殑缂栧彿鏌ユ壘鍒扮浉搴旂殑3D缁撴瀯锛屽苟鍙互灏...
绛旓細娆㈣繋鏉ュ埌鍒嗗瓙瀵规帴鎺㈢储鐨勫濡欎笘鐣岋紝棣栧厛锛岃鎴戜滑娣卞叆鐞嗚ВPDB鏁版嵁搴鈥斺旇繖涓敓鐗╁ぇ鍒嗗瓙缁撴瀯鐨勫疂钘忓簱锛佺敱缇庡浗Brookhaven鍥藉瀹為獙瀹ゅ湪1971骞村垱绔嬶紝鐢盧CSB绮惧績缁存姢鐨凱DB锛圥rotein Data Bank锛夛紝鏄叏鐞冪敓鐗╁垎瀛愮粨鏋勭爺绌剁殑鏍稿績骞冲彴锛屽畠鏀剁撼浜嗘棤鏁拌泲鐧借川銆佹牳閰稿拰绯栫被鐨勪笁缁寸粨鏋勶紝杩欎簺閮芥槸绉戝瀹朵滑閫氳繃X灏勭嚎鍗曟櫠琛嶅皠銆佹牳...
绛旓細鍦拌川PDB鎸囩殑鏄滃湴鐞冨寲瀛︽牱鍝佹暟鎹簱鈥濓紙PetDB锛夛紝鏄竴涓棬鍦ㄦ敹闆嗗拰鎻愪緵鍏ㄧ悆娴锋磱銆侀檰鍦板拰澶ф皵涓湴鐞冨寲瀛﹀拰鍦拌川瀛︽暟鎹殑寮鏀捐闂暟鎹簱銆傝繖涓暟鎹簱鏄敱缇庡浗鍥藉绉戝鍩洪噾浼氳祫鍔╃殑锛屾棬鍦ㄤ负鍏ㄧ悆鍦扮悆绉戝瀹朵滑鎻愪緵涓涓己澶х殑宸ュ叿锛屼互淇冭繘娴锋磱鍜岄檰鍦板湴鐞冨寲瀛﹂鍩熺殑鐮旂┒鍜屾帰绱鍦拌川PDB鍖呭惈浜嗗叏鐞冨涓湴璐ㄦ椂鏈鍜屽绉嶄笉...
绛旓細PDB锛屽嵆"Parallel DataBase"鐨勭缉鍐欙紝鍏朵腑鏂囪В閲婁负鈥滃苟琛鏁版嵁搴鈥濄傝繖涓湳璇湪璁＄畻鏈虹瀛︿腑琚箍娉涗娇鐢紝灏ゅ叾鍦ㄦ暟鎹簱绯荤粺鐨勮璁″拰瀹炵幇涓崰鎹噸瑕佸湴浣嶃侾DB鐨勮嫳鏂囧崟璇嶇洿璇戜负鈥滃苟琛屾暟鎹簱绯荤粺鈥濓紝鍏舵嫾闊充负鈥渂矛ng x铆ng sh霉 j霉 k霉鈥濓紝鍦ㄨ绠楁満棰嗗煙鐨勭缉鍐欒瘝涓紝鍏舵祦琛屽害杈惧埌浜1080锛屼富瑕佸簲鐢ㄤ簬璁＄畻鍜岄┍鍔ㄧ▼搴...
绛旓細1銆PDB鍏ㄧО涓篜luggable Database锛屽嵆鍙彃鎷鏁版嵁搴 2銆丆DB鍏ㄧО涓篊ontainer Database锛屼腑鏂囩炕璇戜负鏁版嵁搴撳鍣紝涓涓暟鎹簱瀹瑰櫒锛圕DB锛夋壙杞藉涓彲鎻掓嫈鏁版嵁搴擄紙PDB锛夊尯鍒簩锛氱敤鎴蜂娇鐢ㄦ椂瀛樻斁浣嶇疆涓嶅悓 1銆丆OMMON USERS(鏅氱敤鎴)锛氱粡甯稿缓绔嬪湪CDB灞傦紝鐢ㄦ埛鍚嶄互C##鎴朿##寮澶达紱2銆 LOCAL USERS(鏈湴鐢ㄦ埛)锛氫粎寤虹珛...
绛旓細PDB鏄洰鍓嶆渶涓昏鐨勬敹闆嗙敓鐗╁ぇ鍒嗗瓙(铔嬬櫧璐ㄣ佹牳閰稿拰绯)2.5缁达紙浠ヤ簩缁寸殑褰㈠紡琛ㄧず涓夌淮鐨勬暟鎹級缁撴瀯鐨鏁版嵁搴,鏄氳繃X灏勭嚎鍗曟櫠琛嶅皠銆佹牳纾佸叡鎸佺數瀛愯灏勭瓑瀹為獙鎵嬫纭畾鐨勮泲鐧借川銆佸绯栥佹牳閰搞佺梾姣掔瓑鐢熺墿澶у垎瀛愮殑涓夌淮缁撴瀯鏁版嵁搴撱傞殢鐫鏅朵綋琛嶅皠鎶鏈殑涓嶆柇鏀硅繘,缁撴瀯娴嬪畾鐨勯熷害鍜岀簿搴︿篃閫愭鎻愰珮銆90骞翠唬浠ユ潵,闅忕潃澶氱淮...
绛旓細浠ヤ笅鍏充簬PDB鏁版嵁搴鎻忚堪姝ｇ‘鐨勬槸锛欰.PDB鏁版嵁搴撴槸涓绾ц泲鐧借川鏁版嵁搴 B.PDB鏁版嵁搴撳瓨鍌ㄥぇ鍒嗗瓙鐨3D缁撴瀯 C.PDB鏁版嵁搴撻噷鏃㈠寘鍚泲鐧借川鐨3D缁撴瀯锛屼篃鍖呭惈鏍搁吀鐨3D缁撴瀯锛屼互鍙婁簩鑰呯殑澶嶅悎浣撶粨鏋 D.PDB鏁版嵁搴撻噷鍙寘鍚疄楠屾柟娉曡В鏋愮殑澶у垎瀛3D缁撴瀯 E.PDB鏁版嵁搴撴槸浜岀骇铔嬬櫧璐ㄦ暟鎹簱 F.PDB鏁版嵁搴撳彧鍌ㄥ瓨铔嬬櫧璐ㄥ垎瀛愮殑3D...
绛旓細PDB鍏ㄧО涓篜luggable Database锛屽嵆鍙彃鎷旀暟鎹簱銆傛墦寮PDB鏁版嵁搴鐨勬柟娉曟湁涓ょ锛氭柟寮1锛歋QL> alter pluggable database PDBEPPS open;Pluggable database altered.SQL> select con_id, dbid, guid, name , open_mode from v$pdbs;CON_ID DBID GUID NAME OPEN_MODE --- --- --- --- --...
