Biocomputing, Institut für Molekulare Biotechnologie (IMB),
Beutenbergstr. 11,
D-07745 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 [1]. It consists basically of two divisions. The Atlas of Macromolecule Structures provides access to all structure entries deposited at the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). An additional division on Basic Information on Biological Macromolecules includes, for example, the Amino Acid Repository, the Base Pair Directory, information on Nucleic Acids Nomenclature and Structure as well as on Structural Elements in Proteins. Finally, introductions to X-ray crystallography, NMR spectroscopy, Fourier Transform Infrared Spectroscopy and Circular Dichroism are available.
Given the increasing number of known three-dimensional biopolymer structures and with the data explosion in other fields of biology there is an urgent need for classification systems and for up-to-date and reliable cross-referencing schemes to other databases. Therefore, we have developed the Hetero Components and Site Databases. They include an environment option that allows to search, for example, for all entries with ligands surrounded by a particular amino acid pattern. The Hetero Components Database offers a Periodical Table Element Browser. Clicking on a particular element symbol generates a list of all PDB entries with a particular metal ion or any other atom, for example.
A comprehensive bending classification of nucleic acid structures is based on a uniform approach for analyzing the bending properties of nucleic acids. It offers for currently more then 900 nucleic acid structures tables listed by the extent of bending or by the shape of the helical axis.
The IMB Jena Image Library of Biological Macromolecules attempts to provide as much information as possible on a particular structure in one place. Therefore, the atlas pages include links to almost 30 other databases. They include many databases with sequence and structural information but also such a data resource like OMIM with disease-related information. Many database links are based on SWISS-PROT/PDB cross references. We have developed a new cross reference scheme that takes into account information from both SWISS-PPROT and PDB and is thus more comprehensive than the schemes provided by either of these databases alone. The search option allows for a direct search of PDB entries via their SWISS-PROT entry names or accession numbers. Partial string matching searches of the SWISS-PROT entry names generate easily comprehensive tables of PDB entries for a particular species or protein type.