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At least 253 records · Page 14Linked to original sources
PubMed2006

A comprehensive dictionary of protein accession codes for complete protein accession identifier alias resolving.

In mass spectrometry-based proteomics, protein identification results usually consist of peptide sequences and database-dependent accession identifiers of the matching proteins. Often certain annotations are only available in particular databases that in turn must be queried by a certain identifier. In order to simplify and unify the tracing of identified proteins back to their original annotation information, a system capable of set-oriented mapping the different accession identifiers of proteins derived from multiple sequence database sources has been developed. This allows unification of the access to protein information and tracing to other online resources providing additional information as well as resolving cross-references of protein identifications. The interface of seqDB is available via http://www.protein-ms.de following the link to seqDB.

Database Management Systems↗
PubMed1998

Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches.

Molecular surface areas of proteins are responsible for selective binding of ligands and protein-protein recognition, and are considered the basis for specific interactions between different parts of a protein. This basic principle leads us to study the interfaces within proteins as a learning set for intermolecular recognition processes of ligands like substrates, coenzymes, etc., and for prediction of contacts occurring during protein folding and association. For this purpose, we defined interfaces as pairs of matching molecular surface patches between neighboring secondary structural elements. All such interfaces from known protein structures were collected in a comprehensive data bank of interfaces in proteins (DIP). The up-to-date DIP contains interface files for 351 selected Brookhaven Protein Data Bank entries with a total of about 160,000 surface elements formed by 12,475 secondary structures. For special purposes, the inclusion of additional structures or selection of subgroups of proteins can be performed in an easy and straightforward manner. Atomic coordinates of the constituents of molecular surface patches are directly accessible as well as the corresponding contact distances from given atoms to their neighboring secondary structural elements. As a rule, independent of the type of secondary structure, the molecular surface patches of the secondary structural elements can be described as quite flat bodies with a length to width to depth ratio of about 3:2:1 for patches consisting of more than ten atoms. The relative orientation between two docking patches is strongly restricted, due to the narrow distribution of the distances between their centers of mass and of the angles between their normal lines, respectively. The existing retrieval system for the DIP allows selection (out of the set of molecular patches) according to different criteria, such as geometric features, atomic composition, type of secondary structure, contacts, etc. A fast, sequence-independent 3-D superposition procedure was developed for automatic searches for geometrically similar surface areas. Using this procedure, we found a large number of structurally similar interfaces of up to 30 atoms in completely unrelated protein structures.

Databases, Factual↗
PubMed2000

A study of the references used in Cochrane protocols and reviews. Three bibles, three dictionaries, and nearly 25,000 other things.

OBJECTIVES: To describe the types of report that are cited by protocols and reviews included in the Cochrane Database of Systematic Reviews. METHODS: The citation for each reference included in the Cochrane protocols and reviews published in the Cochrane Database of Systematic Reviews in issue 1, 1999 of The Cochrane Library were categorized by reference type (e.g., journal article, conference proceeding, book chapter, personal communication, Cochrane review). RESULTS: Of a total of 24,913 citations, 21,694 (87.1%) were references to journal articles. There was a significant difference between the proportion of references to studies that were journal articles (12,348 of 13,472; 91.7%) and the proportion of other references in this category (9,346 of 11,441; 81.7%). CONCLUSION: The great majority of studies included in Cochrane reviews at the beginning of 1999 had been published as journal articles.

Clinical Protocols↗
PubMed2002

SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. Additional facilities include a data mining query tool, graphical database administration tools, and a NMRStar v2. 1.1 file generator. SPINS also includes a user-friendly internet-based graphical user interface, which is optionally integrated with Varian VNMR NMR data collection software. This paper provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and an outline of future plans for the SPINS project.

Archives↗