14 Mar 2012

Protein Structure Resources

Databases described in this section can provide a better understanding of what a gene's protein product looks like. For some well-studied proteins, users also may find structures of mutant forms that can be compared with structures of nonmutated or wild-type proteins.

A good, basic introduction to protein structures, X-ray crystallography, and nuclear magnetic resonance spectroscopy (NMR) can be found in the National Institute of General Medical Sciences (NIGMS) 2001 publication The Structures of Life (67 pp.). A free copy can be ordered from the NIGMS Publication List or downloaded as a PDF file (requires Adobe Acrobat Reader).

For more information:

Nature of 3-D Structural Data: The Protein Data Bank's brief introduction to X-ray crystallography and NMR

Crystallography 101: Tutorial by Dr. Bernhard Rupp at Lawrence Livermore National Laboratory

The Basics of NMR: Online text book by Dr. Joseph P. Hornak, professor of Chemistry and Imaging Science at the Rochester Institute of Technology

Indication: Protein Data Bank (PDB) is an international archive of 3D structural information for biological macromolecules. PDB is managed by the Research Collaboratory for Structural Bioinformatics (RCSD), a nonprofit consortium involving Rutgers, the State University of New Jersey; National Institute of Standards and Technology (NIST); and San Diego Supercomputer Center at the University of California, San Diego.

Examination Tips: Users can query the archive by PDB ID or keyword using the search box on the main page. Other query options include SearchLite (keyword search form with examples), SearchFields (an advanced search option with customizable fields), and Status Search (used to find structures being processed by PDB). To learn more about searching PDB, take the Query Tutorial or examine the User Guides.

Info Provided: Each structure record includes a summary, structure viewing options, download and display options, links to records of structural neighbors, geometry, links to other protein information sources, and details about the structure's sequence. For step-by-step instructions on interacting with 3-D structures, see Examining a Protein's Structure.

Indication: The National Center for Biotechnology Information (NCBI) database of three-dimensional molecular structure is called the Molecular Modeling Database (MMDB). The database is searchable via NCBI's Entrez retrieval system. Structure data is derived from X-ray crystallography and Nuclear Magnetic Resonance (NMR) structure determinations from Protein Data Bank (PDB). This database is considerably smaller than Entrez's nucleotide and protein sequence databases. If a structure for a known sequence is not included, the structure of a protein homolog may be available for examination.

Exploration Tips: Users can use the query interface to search by keyword, or access structure records directly through links in PubMed citations and nucleotide and protein sequence records. Links to instructions for searching by keyword, protein sequence, and nucleotide sequence are on the main search page. As in other Entrez databases, users can refine searches using fields available in Limits, preview query results and browse index terms in Preview/Index, combine searches using History, and store selected records from different searches on Clipboard. Some indexed fields that can be used to narrow a search include accession number, substance name, author name, journal name, organism, properties, and text word. Boolean Operators AND, OR, and NOT must be in upper case. Phrase searching using double quotes and truncation using the asterisk (*) as a wild card also are supported. For more information about searching this and other NCBI Entrez databases, see the Entrez Help Document.

Info provided: Each structure record or summary includes MMDB and PDB identifiers, links to protein and nucleotide sequences and related MEDLINE documents, taxonomy assignments, structure authors, date the structure was deposited into PDB, PDB classification and macromolecular content, links to sequence and structure neighbors, and structure-viewing options. Entries in MMDB are cross-linked to bibliographic information, sequence database entries, and NCBI taxonomy. To view a structure, users must download NCBI's free 3D structure viewer Cn3D, which is supported by Windows, Macintosh, and UNIX platforms. To learn more about using this viewer, see NCBI's Cn3D Tutorial, Help, and FAQs.

View-Article-Sources: http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/geneguide.shtml#structure

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