Go to the abstract in the NAR 2002 Database Issue.
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http://www.imb-jena.de/IMAGE.html
Reichert, J., Suehnel, J.
Biocomputing Group Institut fuer Molekulare Biotechnologie Postfach 100813 D-07708 Jena / Germany
Contact jsuehnel@imb-jena.de
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. 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. By combining automatic and manual processing it is possible to keep pace with the rapidly growing number of known biopolymer structures and to provide information not available from automatic procedures for selected entries. With the increasing number of structures the generation of classification schemes and of relationships between different entries become 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 helix and bending analysis tool provides consistent information on more than 900 DNA and RNA duplex structures. 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 information as possible in one place.
The Image Library was extended by a site database. A newly developed analysis tool identifies all residues surrounding hetero components or sites according to geometrical criteria. This enables one to search for all structures with a certain pattern of amino acids/nucleotides/water adjacent to hetero components or sites. A new PDB/SWISS-PROT cross reference scheme combines information from both PDB and SWISS-PROT. Searching can now be done via PDB and NDB codes as well as via SWISS-PROT entry names/accession numbers. Each atlas page contains a listing of related protein entries sharing the same protein chain(s). The PDB/SWISS-PROT cross reference database can be used to generate PDB entry tables listed by SWISS-PROT protein or species names. The existing brief descriptions of X-ray, NMR and FTIR methods for structure determination are now supplemented by information on circular dichroism. The number of databases linked to the atlas pages is further increased and includes also relatively new data resources, such as INTERPRO and SMART, that are not yet taken into account by other structure databases. Finally, a new tool allows for the visualization of user-supplied files.
Category Structure
Go to the abstract in the NAR 2002 Database Issue.