A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules.
The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Library of Biological Macromolecules--JenaLib. Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data. Here, we briefly describe these resources from a user's point of view and from a comparative perspective. It is our aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources.
Hühne
Rolf
R
Biocomputing Group, Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Jena Centre for Bioinformatics, Beutenbergstr 11, D-07745 Jena/Germany.
Koch
Frank-Thomas
FT
Sühnel
Jürgen
J
D000595:Amino Acid Sequence; D003196:Computer Graphics; D016208:Databases, Factual; D030562:Databases, Protein; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid
D046911:Macromolecular Substances; D011506:Proteins