Jenalib: Jena Library of Biological Macromolecules
NAR Molecular Biology Database Collection entry number 267
Reichert, J., Suehnel, J.
Biocomputing Group, Institut fuer Molekulare Biotechnologie, Postfach 100813, D-07708 Jena, Germany
The IMB Jena Image Library of Biological Macromolecules (http://www.imb-jena.de/IMAGE.html) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). In addition, basic information on the architecture of biological macromolecules and brief descriptions of experimental methods in structure determination are offered. By combining automatic and manual processing it is possible both to keep pace with the rapidly growing number of known biopolymer structures and to provide information not available from automatic procedures at least for selected entries. A variety of visualization and analysis tools for complete molecules as well as for parts of molecules, such as hetero components, sites and cis-peptide bonds, are available for each entry. The database can be accessed either by search options or by browsing precomputed or dynamically generated entry tables. In addition to the search for PDB or NDB codes and a full-text search of the structure file header, searching for entry names/accession numbers, species names, gene names and entry descriptions from SWISS-PROT and also for NCBI species names, Pfam family names and SMART domain names is possible. With the increasing number of structures the generation of classification schemes and of relationships between different entries becomes more and more important. Among other tools the built-in hetero components and site databases help to accomplish this aim. A PDB/SWISS-PROT cross reference scheme takes into account cross reference information provided by both the PDB and SWISS-PROT. By means of this scheme PDB structure tables listed by SWISS-PROT protein or species names can be generated. A genus/species classification provides compilations of structure entries for species listed by frequency of occurrence in the PDB or by the deposition data of the very first structure for a particular species (PDB Structure Species Timeline). A helix and bending analysis tool provides consistent information on all DNA and RNA structures with at least 6 successive base pairs. These data are used for a comprehensive bending classification of nucleic acid structures. Finally, a steadily increasing number of links to other databases helps to provide as much useful information as possible in one place.
The IMB Jena Image Library now offers substantially extended search options. In addition to the old search for PDB or NDB codes and a full-text search of the structure file header they allow to search for entry names/accession numbers, species names, gene names and entry descriptions from SWISS-PROT, but also for NCBI species names, Pfam family names and SMART domain names. A new genus/species classification provides PDB structures genus or species tables listed by genus/species name, number of structures known for a genus/species and deposition data for the very first structure of a particular genus/species (timeline). By means of a new Gene Ontology (GO)interface to the PDB structures are directly mapped to GO term names.
Category: Structure Databases
Subcategory: Protein structure
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