Protein Data Bank

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Protein Data Bank

  1. 1. WWW.RCSB.ORG/PDB
  2. 2. • Introduction• Supported and funded by• History• PDB Holdings list• Member organizations• Task forces• PDB ID• PDB File format• Browse to WWW.RCSB.ORG/PDB/
  3. 3.  “The repository reservoir data bank to store the authenticated structures of Protein and Nucleic acid” Single worldwide database and hundreds of secondary databases categorize the data differently. Key resource in the area of structural biology, stores 3D structural data of large biological molecules such as Proteins and Nucleic acids. Data is submitted by Biologists and Biochemists from all around the world to be freely accessible on internet via its member organizations’ websites and is updated weekly. The mission is to maintain a single Protein Data Bank Archive of Macromolecular Structural data.
  4. 4.  The Protein Data Bank (PDB) is operated by: Rutgers, The State University of New Jersey. The San Diego Supercomputer Center at the University of California, San Diego. RCSB-the Research Collaborator for Structural Bioinformatics The PDB is supported by funds from the National Science Foundation, the Department of Energy, and the National Institutes of Health.
  5. 5. Two forces to initiate PDB: Growing collection of sets of protein structural data by X-Ray diffraction. NMR-nuclear Magnetic Resonance method to visualize protein structures in 3D, emerged in 1968. In 1969, Dr Edger Meyer began to write software to store atomic coordinates files in a common format to make them available for geometric and graphical evaluation. In 1971, one of Dr Meyer’s programs- SEARCH- enabled networking i.e enabled the researchers to access information from database to study protein structures offline.
  6. 6.  In 1973, upon Hamilton’s death, Dr Tom Koetzle took over direction of PDB for 20 years. mmCIF project completed and Structural genomics began in 1970s. In 1980s, IUCr guidelines established, number of structures deposited increases and independent biological databases established – e.g., the NDB. In Oct, 1998; PDB was transferred to Research Collaboratory for Structural Bioinformatics (RCSB), complete transfer since 1999. Dr Helen M Berman of Rutgers University was the new director. In 2003, with the formation of wwPDB, the PDB became an international organization having three member organizations. In 2006, the BMRB joined PDB.
  7. 7. Experimental Protein/Nucleic Acid Proteins Nucleic Acids Other Total Method complexesX-ray diffraction 62750 1323 3050 2 67125NMR 7962 960 179 7 9108Electron microscopy 262 22 96 0 380Hybrid 41 3 1 1 46Other 133 4 5 13 155 Total: 71148 2312 3331 23 76814
  8. 8.  Act as Data deposition, Data processing and Distribution centers for PDB data. Three are founding member organizations: PDBe…Protein Data Bank in Europe. PDBj…Protein Data Bank in Japan. RCSB…Research Collaboratory for Structural Bioinformatics. The Biological Magnetic Resonance Data Bank (BMRB) joined later in 2006. Another organization Worldwide Protein Data Bank (wwPDB) oversees PDB. wwPDB reviews and annotates each submitted entry and then it is automatically checked for plausibility( the source code) for validation software is available.
  9. 9.  X-Ray diffraction :-Spacing of atoms determined by location intensities spot on photographic plate by X-Ray e.g lyzozyme. Limited to just crystal structures only NMR (about 15% e.g., hemoglobin)…estimations of distances between pairs of atoms of proteins. Final conformation is obtained after solving distance geometry problem. Illuminate dynamic side,conformatonal changes, protein folding as well
  10. 10.  Each structure published in PDB receives a four character alphanumeric identifier or accession number. Like, 1ANG or 4hhb. However, this cant be used as an identifier for biomolecules. Because several structures for the same molecule in different environments or conformations-are contained in PDB with different PDB IDs. HAEMOGLOBIN (2DN2)
  11. 11.  Standard data representation…encoded in data dictionary. The metadata model supporting this representation is used by all PDB data processing and database software tools.1. PDB file format was restricted to 80 characters per line initially.2. In 1996, macromolecular Crystallographic Information File (mmCIF) format started.3. In 2005, XML version called as PDBML, was described.
  12. 12.  The Protein Data Bank (pdb) file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank. provides description and annotation structure  atomic coordinates,  side chains,  secondary structure, as well as  atomic connectivity Water , ions, nucleic acids, ligands…
  13. 13.  mmCIF is the acronym for the macromolecular Crystallographic Information File. mmCIF is based on a subset of the syntax rules for the Self Defining Text Archive (STAR) file. A Dictionary Description Language (DDL) defines the structure of mmCIF dictionaries. Dictionaries provide the metadata which define the content of mmCIF data files. mmCIF data files, dictionaries and DDLs are all expressed in a common syntax.
  14. 14.  basic information, more detailed description of PDB, PDBML and mmCIF file formats can be found at Protein Data Bank web sites. highly recommended to get familiar with all rules of PDB format (such as gaps between columns) BEACAUSE…
  15. 15. put either a search term (for example, a protein name) or a PDB number
  16. 16. 2DN2
  17. 17. HAEMOGLOBIN
  18. 18.  If the contents of the PDB are thought of as primary data,THEN hundreds of derived (i.e., secondary) databases categorize the data differently.For example SCOP & CATH :  categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.
  19. 19. The Structural Classification ofProteins (SCOP) database is alargely manual classification ofprotein structural domains basedon similarities oftheir structures and aminoacid sequences
  20. 20. Class:the overall secondary-structure content of thedomainArchitecture:high structural similarity but no evidenceof homology.Topology:a large-scale grouping of topologies whichshare particular structural featuresHomologous superfamily:indicative of a demonstrableevolutionary relationship.
  21. 21. Pfam is a databaseof proteinfamilies thatincludes theirannotationsand multiplesequencealignmentgeneratedusing hiddenMarkov models
  22. 22. CLICK
  23. 23. Select your desiremethod
  24. 24. CLICK
  25. 25. CLICK
  26. 26. CLICK
  27. 27. CLICK
  28. 28. & FINALLY
  29. 29. Show the gradual updatingStructural View of Biology released entries
  30. 30. You can alsoselect differentdisplay view
  31. 31. can also download indifferent view
  32. 32.  Text file can be viewed or modified in editor. Structure files may be viewed using various free and commercial visualizations programs and Web browsers plug-ins like OPEN SOURCE PDB SOFTWERES Jmol Molekel MeshLab (able to import PDB data set and buildup surfaces from them) QuteMol Avogadro OPEN BUT NOT FREE PYMOL , RASMOL, VIST PROT 3DS & STAR BIOCHEM
  33. 33. The RCSB PDB website containsan extensive list of both free andcommercial molecule visualizationprograms and web browser plug-in.
  34. 34.  central archive of experimentally solved bimolecular structures. But only allows data retrieval does not provide collaboration or user feedback. In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. provides tools for discussing and annotating proteins in a collaborative way.
  35. 35.  The Protein Data Bank (PDB) is the central archive of experimentally solved bimolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback. In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. It provides tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely-accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation.
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