Protein Circular Dichroism Data Bank (PCDDB): data bank and website design. 2006

Lee Whitmore, and Robert W Janes, and B A Wallace
Dept. of Crystallography, Birkbeck College, University of London, London, UK.

The Protein Circular Dichroism Data Bank (PCDDB) is a new deposition data bank for validated circular dichroism spectra of biomacromolecules. Its aim is to be a resource for the structural biology and bioinformatics communities, providing open access and archiving facilities for circular dichroism and synchrotron radiation circular dichroism spectra. It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures. In this article, we discuss the design of the data bank structure and the deposition website located at http://pcddb.cryst.bbk.ac.uk. Our aim is to produce a flexible and comprehensive archive, which enables user-friendly spectral deposition and searching. In the case of a protein whose crystal structure and sequence are known, the PCDDB entry will be linked to the appropriate PDB and sequence data bank files, respectively. It is anticipated that the PCDDB will provide a readily accessible biophysical catalogue of information on folded proteins that may be of value in structural genomics programs, for quality control and archiving in industrial and academic labs, as a resource for programs developing spectroscopic structural analysis methods, and in bioinformatics studies.

UI MeSH Term Description Entries
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D002942 Circular Dichroism A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Circular Dichroism, Vibrational,Dichroism, Circular,Vibrational Circular Dichroism
D013056 Spectrophotometry, Ultraviolet Determination of the spectra of ultraviolet absorption by specific molecules in gases or liquids, for example Cl2, SO2, NO2, CS2, ozone, mercury vapor, and various unsaturated compounds. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Ultraviolet Spectrophotometry
D014584 User-Computer Interface The portion of an interactive computer program that issues messages to and receives commands from a user. Interface, User Computer,Virtual Systems,User Computer Interface,Interface, User-Computer,Interfaces, User Computer,Interfaces, User-Computer,System, Virtual,Systems, Virtual,User Computer Interfaces,User-Computer Interfaces,Virtual System
D016208 Databases, Factual Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references. Databanks, Factual,Data Banks, Factual,Data Bases, Factual,Data Bank, Factual,Data Base, Factual,Databank, Factual,Database, Factual,Factual Data Bank,Factual Data Banks,Factual Data Base,Factual Data Bases,Factual Databank,Factual Databanks,Factual Database,Factual Databases
D016247 Information Storage and Retrieval Organized activities related to the storage, location, search, and retrieval of information. Information Retrieval,Data Files,Data Linkage,Data Retrieval,Data Storage,Data Storage and Retrieval,Information Extraction,Information Storage,Machine-Readable Data Files,Data File,Data File, Machine-Readable,Data Files, Machine-Readable,Extraction, Information,Files, Machine-Readable Data,Information Extractions,Machine Readable Data Files,Machine-Readable Data File,Retrieval, Data,Storage, Data
D017356 Synchrotrons Devices for accelerating protons or electrons in closed orbits where the accelerating voltage and magnetic field strength varies (the accelerating voltage is held constant for electrons) in order to keep the orbit radius constant. Synchrotron
D017510 Protein Folding Processes involved in the formation of TERTIARY PROTEIN STRUCTURE. Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular
D019295 Computational Biology A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets. Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D020407 Internet A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange. World Wide Web,Cyber Space,Cyberspace,Web, World Wide,Wide Web, World

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