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Structure database: PDB

Structure database: PDB. Tuomas Hätinen. Protein Data Bank. A repository for 3-D biological macromolecular structure. It includes proteins, nucleic acids and viruses. Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%). Protein Data Bank.

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Structure database: PDB

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  1. Structure database: PDB Tuomas Hätinen

  2. Protein Data Bank • A repository for 3-D biological macromolecular structure. • It includes proteins, nucleic acids and viruses. • Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%).

  3. Protein Data Bank • Founded in 1971 by Brookhaven National Laboratory, New York. • Transferred to the Research Collaboratory for Structural Bioinformatics (RCSB) in 1998. • Currently it holds 40,000 released structures.

  4. Protein Data Bank

  5. PDB data formats • PDB file format was used to contain the coordinates and related information. • In the late 1990’s, macromolecular Crystallographic Information file (mmCIF) evolved. • mmCIF and PDBML • Push in to make structure files completely self-contained descriptions of the experiment and details of the structure determination. • PDB file format unstructured and obsolete

  6. PDB File Format • Text file – you can edit with a text editor e.g. WordPad • Atomic co-ordinates • Rich annotation • Citation • Experimental Method • Biological source e. • Etc.

  7. Demo & Exercises

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