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PDBsum

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in October 2012, all single amino acid variants identified by the project have been mapped to the corresponding protein sequences in the Protein Data Bank. These variants are also displayed within PDBsum, cross-referenced to the relevant
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Each structure in the PDBsum database includes an image of structure (main view, Bottom view and right view), molecular components contained in the complex(structure), enzyme reaction diagram if appropriate,
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Laskowski RA, Hutchinson EG, Michie AD, Wallace AC, Jones ML, Thornton JM (Dec 1997). "PDBsum: a Web-based database of summaries and analyses of all PDB structures".
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domain assignments, description of bound molecules and graphic showing interactions between protein and secondary structure, schematic diagrams of
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Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC,
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molecular graphics software are used to provide a 3D view of molecules and their interactions within PDBsum.
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The original version of the database was developed around 1995 by Roman Laskowski and collaborators at
219: 359:"PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids" 228: 56: 569: 516: 437: 388: 339: 290: 164: 102: 43: 559: 551: 535: 506: 498: 427: 419: 378: 370: 329: 321: 282: 235:. One branch of PDBsum, known as DrugPort, focuses on these models and is linked with the 78: 207:, analysis of clefts contained within the structure and links to external databases. The 564: 539: 511: 486: 432: 407: 180: 179:. As of 2014, PDBsum is maintained by Laskowski and collaborators in the laboratory of 383: 358: 286: 603: 334: 309: 192: 160: 232: 461:. European Molecular Biology Laboratory – The European Bioinformatics Institute 573: 520: 441: 392: 343: 325: 555: 294: 106: 502: 423: 374: 236: 200: 63: 26: 224: 540:"DrugBank 3.0: a comprehensive resource for 'omics' research on drugs" 208: 159:
is a database that provides an overview of the contents of each 3D
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Pictorial database of 3D structures in the Protein Data Bank
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de Beer TA, Berka K, Thornton JM, Laskowski RA (Jan 2014).
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Laskowski RA, Chistyakov VV, Thornton JM (Jan 2005).
195:functional assignments, a 1D sequence annotated by 144: 139: 117: 112: 98: 90: 77: 72: 62: 50: 38: 33: 310:"PDBsum: summaries and analyses of PDB structures" 42:Overview of the structures contained within the 480: 478: 476: 453: 451: 8: 19: 18: 563: 510: 431: 382: 333: 615:Science and technology in Cambridgeshire 227:identifier. PDBsum contains a number of 265: 7: 595:. European Bioinformatics Institute. 459:"PDBsum documentation: About PDBsum" 14: 185:European Bioinformatics Institute 84:European Bioinformatics Institute 94:Roman Laskowski & al. (1997) 25: 275:Trends in Biochemical Sciences 1: 620:South Cambridgeshire District 287:10.1016/S0968-0004(97)01140-7 550:(Database issue): D1035-41. 205:protein–protein interactions 610:Protein structure databases 591:Laskowski RA, Thornton JM. 233:structure-based drug design 231:that may be of interest in 163:structure deposited in the 636: 497:(Database issue): D292-6. 418:(Database issue): D355-9. 369:(Database issue): D266-8. 254:Protein structure database 406:Laskowski RA (Jan 2009). 308:Laskowski RA (Jan 2001). 249:Crystallographic database 218:Since the release of the 177:University College London 24: 544:Nucleic Acids Research 491:Nucleic Acids Research 412:Nucleic Acids Research 363:Nucleic Acids Research 314:Nucleic Acids Research 239:drug target database. 326:10.1093/nar/29.1.221 220:1000 Genomes Project 556:10.1093/nar/gkq1126 408:"PDBsum new things" 21: 593:"PDBsum home page" 503:10.1093/nar/gkt940 487:"PDBsum additions" 424:10.1093/nar/gkn860 375:10.1093/nar/gki001 229:protein structures 57:Protein structures 165:Protein Data Bank 154: 153: 44:Protein Data Bank 627: 596: 578: 577: 567: 531: 525: 524: 514: 482: 471: 470: 468: 466: 455: 446: 445: 435: 403: 397: 396: 386: 354: 348: 347: 337: 305: 299: 298: 270: 135: 132: 130: 128: 126: 124: 99:Primary citation 29: 22: 635: 634: 630: 629: 628: 626: 625: 624: 600: 599: 590: 587: 582: 581: 533: 532: 528: 484: 483: 474: 464: 462: 457: 456: 449: 405: 404: 400: 356: 355: 351: 307: 306: 302: 272: 271: 267: 262: 245: 173: 146: 121: 79:Research center 52: 17: 12: 11: 5: 633: 631: 623: 622: 617: 612: 602: 601: 598: 597: 586: 585:External links 583: 580: 579: 526: 472: 447: 398: 349: 300: 281:(12): 488–90. 264: 263: 261: 258: 257: 256: 251: 244: 241: 181:Janet Thornton 172: 169: 161:macromolecular 152: 151: 148: 142: 141: 137: 136: 119: 115: 114: 110: 109: 100: 96: 95: 92: 88: 87: 81: 75: 74: 70: 69: 66: 60: 59: 54: 48: 47: 40: 36: 35: 31: 30: 15: 13: 10: 9: 6: 4: 3: 2: 632: 621: 618: 616: 613: 611: 608: 607: 605: 594: 589: 588: 584: 575: 571: 566: 561: 557: 553: 549: 545: 541: 537: 530: 527: 522: 518: 513: 508: 504: 500: 496: 492: 488: 481: 479: 477: 473: 460: 454: 452: 448: 443: 439: 434: 429: 425: 421: 417: 413: 409: 402: 399: 394: 390: 385: 380: 376: 372: 368: 364: 360: 353: 350: 345: 341: 336: 331: 327: 323: 319: 315: 311: 304: 301: 296: 292: 288: 284: 280: 276: 269: 266: 259: 255: 252: 250: 247: 246: 242: 240: 238: 234: 230: 226: 221: 216: 214: 210: 206: 202: 198: 194: 193:Gene ontology 188: 186: 182: 178: 170: 168: 166: 162: 158: 149: 143: 140:Miscellaneous 138: 134: 120: 116: 111: 108: 104: 101: 97: 93: 89: 85: 82: 80: 76: 71: 67: 65: 61: 58: 55: 49: 45: 41: 37: 32: 28: 23: 547: 543: 538:(Jan 2011). 529: 494: 490: 463:. Retrieved 415: 411: 401: 366: 362: 352: 320:(1): 221–2. 317: 313: 303: 278: 274: 268: 217: 189: 174: 156: 155: 145:Bookmarkable 465:9 September 39:Description 604:Categories 536:Wishart DS 260:References 51:Data types 64:Organisms 574:21059682 521:24153109 442:18996896 393:15608193 344:11125097 243:See also 237:DrugBank 201:InterPro 171:Database 147:entities 53:captured 565:3013709 512:3965036 433:2686501 295:9433130 225:UniProt 187:(EBI). 183:at the 167:(PDB). 131:/pdbsum 118:Website 107:9433130 91:Authors 73:Contact 34:Content 572:  562:  519:  509:  440:  430:  391:  384:539955 381:  342:  332:  293:  209:RasMol 157:PDBsum 113:Access 105:  20:PDBSum 335:29784 86:(EBI) 570:PMID 517:PMID 467:2014 438:PMID 389:PMID 340:PMID 291:PMID 213:Jmol 211:and 199:and 197:Pfam 125:.ebi 103:PMID 560:PMC 552:doi 507:PMC 499:doi 428:PMC 420:doi 379:PMC 371:doi 330:PMC 322:doi 283:doi 150:yes 129:.uk 127:.ac 123:www 68:all 606:: 568:. 558:. 548:39 546:. 542:. 515:. 505:. 495:42 493:. 489:. 475:^ 450:^ 436:. 426:. 416:37 414:. 410:. 387:. 377:. 367:33 365:. 361:. 338:. 328:. 318:29 316:. 312:. 289:. 279:22 277:. 576:. 554:: 523:. 501:: 469:. 444:. 422:: 395:. 373:: 346:. 324:: 297:. 285:: 133:/ 46:.

Index


Protein Data Bank
Protein structures
Organisms
Research center
European Bioinformatics Institute
PMID
9433130
www.ebi.ac.uk/pdbsum/
macromolecular
Protein Data Bank
University College London
Janet Thornton
European Bioinformatics Institute
Gene ontology
Pfam
InterPro
protein–protein interactions
RasMol
Jmol
1000 Genomes Project
UniProt
protein structures
structure-based drug design
DrugBank
Crystallographic database
Protein structure database
doi
10.1016/S0968-0004(97)01140-7
PMID

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