Bioinformatics & Genomics
Compounds & Enzymes
Chemical Viewers & SMILES
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3D Virtual Chemistry Library
[Imperial College of Science, Technology & Medicine] A molecular database that includes structure in several formats, physical data, history and
reactivity of each molecule. This large amount of information provides a better quality resource for the user.
[EBI] This enzyme database contains information about nomenclature, reaction and specificity, enzyme structure, isolation/preparation, stability, literature references, and cross references to sequence and 3D-structure data banks.
Cambridge Structural Database
[Univ. of Cambridge] “The Cambridge Structural Database (CSD) contains crystal structure information for over 220,000 organic and metal organic compounds. All of these crystal structures have been analyzed using X-ray or neutron diffraction techniques.”
Directory of P450-containing Systems
[Degtyarenko and Fabian] The goal of this WWW directory is to facilitate access to electronic resources world wide for all researchers working in the field of P450 proteins and P450-containing systems.
[ExPASy at the Swiss Institute of Bioinformatics] An enzyme nomenclature database based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB).
Enzyme Structures Database
[University College London] A database of the known enzyme structures in the Brookhaven Protein Data Bank.
[Argonne National Laboratories] The EMP database contains detailed information on a very large number of enzymes from over 17,000 articles. It can be searched by name, EC number, taxon, tissue, or organelle.
[AGRO and INRA] A database containing information on the molecular forms, promoters, gene structures, mutations, mutalign, and a variety of tables on cholinesterases and related enzymes.
Gene OntologyTM Consortium
The goal of the Gene OntologyTM Consortium is to produce a dynamic controlled vocabulary
that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
[Uppsala University] The Hetero-compound Information
Centre – Uppsala is a freely-accessible resource for structural biologists dealing with
hetero-compounds (“small molecules”) encountered in files from the Protein Data Bank.
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HIV Protease Database
[The National Cancer Institute] An archive of experimentally determined 3-D structures of Human Immunodeficieny Virus 1 (HIV-1), Human Immunodeficieny Virus 2 (HIV-2), and Simian Immunodeficiency Virus (SIV) proteases and their complexes.
Klotho: Biochemical Compounds Declarative Database
[Institute for Biomedical Computing, Washington University] This database was developed as a beginning attempt to model biological processes. It catalogues biochemical compounds and their properties.
LIGAND: Ligand Chemical Database for Enzyme Reactions and Chemical Compounds
[Kyoto University] Provides linkage between chemical and biological aspects in enzymatic reactions. The database consists of three sections: the ENZYME section, the COMPOUND section, and the REACTION section.
[Ohio State University] A relational database of thermodynamic and associated information on lipid mesophase and crystal polymorphic transitions. Database includes lipid molecular structures.
[Babraham Institute] A database of peptidases, provding a catalogue and structure-based classification.
Nucleic Acid Database
[Rutgers University] (NDB) The Nucleic Acid Database Project (NDB) assembles and distributes structural information about nucleic acids.
[Univ. of Tours, France] A web server specializing in proteases and protease inhibitors.
REBASE: The Restriction Enzyme Database
[New England BioLabs] (Richard Roberts and Dana Macelis) Information on restriction enzymes, methylases, the organisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, availability, and reference material.