The Jena Library of Biological Macromolecules (JenaLib) 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) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. The JenaLib intends to fulfill both scientific and educational needs. ... [Information of the supplier]
The Biomolecular Structure and Modelling group brings together groups which derive protein structural information using crystallography or NMR, those who manage databases of structural information and analysts and modellers who examine these structures to derive principles of protein folding. [Information of the supplier]
The Biological Macromolecule Crystallization Database (BMCD) contains crystal data and the crystallization conditions, which have been compiled from literature. The current version of the BMCD includes 5247 crystal entries from macromolecules for which diffraction quality crystals have been obtained. These include proteins, protein:protein complexes, nucleic acid, nucleic acid:nucleic acid complexes, protein:nucleic acid complexes, and viruses. ... [Information of the supplier]
BRENDA is the main collection of enzyme functional data available to the scientific community. It is available free of charge for academic, non-profit users via the internet and as an in-house database for commercial users (requests to our distributor Biobase). Today, as the large international genome sequence projects are gaining a great amount of public attention and huge sequence data bases are created it becomes more and more obvious that we are very limited in our ability to access functional data for the gene products - the proteins, in particular for enzymes. Those data are inherently very difficult to collect, interpret and standardize as they are highly distributed among journals from different fields and are often subject to experimental conditions. Nevertheless a systematic collection is essential for our interpretation of the genome information and more so for possible applications of this knowledge in the fields of medicine, agriculture, etc.. Recent progress on enzyme immobilisation, enzyme production, enzyme inhibition, coenzyme regeneration and enzyme engineering has opened up fascinating new fields for the potential application of enzymes in a large range of different areas. The enzymes are classified according to the Enzyme Commission list of enzymes. Some 3500 "different" enzymes are covered. Frequently enzymes with very different properties are included under the same EC number. Although we intend to give a representative overview on the characteristics and variability of each enzyme the Handbook is not a compendium. The reader will have to go to the primary literature for more detailed information. Naturally it is not possible to cover all the numerous literature references for each enzyme (for some enzymes up to 40000) if the data representation is to be concise as is intended. The data collection is being developed into a metabolic network information system with links to Enzyme expression and regulation information. ... [Information of the supplier]
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms. ChEBI encompasses an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ... [Information of the supplier]
InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. [Information of the supplier]
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The Summary page describing a given peptidase can be reached by use of an index under its Name, MEROPS Identifier or source Organism. The Summary describes the classification and nomenclature of the peptidase and offers links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. ... [Information of the supplier]
The Molecular Modeling Database (MMDB) contains 3D macromolecular structures, including proteins and polynucleotides. MMDB contains over 28,000 structures and is linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors. [Information of the supplier]
MPtopo is a curated database of membrane proteins with experimentally validated transmembrane (TM) segments. The database is maintained in SQL form using the MySQL server. It can be searched using MPtopoQuerier, a java applet developed for this purpose. Retrieved sequences can be examined automatically by MPEx, a java-based hydropathy-plot tool. MPtopo currently contains a total of 167 proteins with 1028 TM segments. ... [Information of the supplier, modified]
The Nuclear Protein Database (NPD) is a searchable database of information on proteins that are localised to the nucleus of vertebrate cells. The NPD contains information on >1000 vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms. Where appropriate, links to other databases are provided. ... [Information of the supplier]
