DATABASES ON MEDICINE AND MOLECULAR BIOLOGY
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Amino Acid Indices And Similarity Matrices
 

Database about physicochemical properties of amino acids.
http://www.genome.ad.jp/aaindex/

The A to Z of Materials
 

The idea to launch AZoM.com originated in late 1999 from a group of materials scientists from the UK, Canada and Australia, who fully appreciated the potential of Advanced Materials but who were frustrated by the lack of awareness of the end-user community.
http://www.azom.com/

Online Maps of Metabolic and Signaling Pathways
 

Graphical display of pathways.
http://www.biocarta.com

The University of Minnesota Biocatalysis / Biodegradation Database"  info
 

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
http://eawag-bbd.ethz.ch/

Biochemical Nomenclature Committees
 

Nomenklatur by the International Union of Pure and Applied Chemistry and by the International Union of Biochemistry and Molecular Biology.

http://www.chem.qmul.ac.uk/iupac/jcbn/

Biochemical Pathways (Roche)
 

Graphical display of biochemical pathways.
http://www.expasy.org/cgi-bin/search-biochem-index

BioCyc Open Chemical Database
 

The BioCyc Open Chemical Database (BOCD) is a collection of chemical compound data from the BioCyc databases. Most of the compounds act as substrates in enzyme-catalyzed metabolic reactions, but some compounds serve as enzyme activators, inhibitors, or cofactors. Chemical structures are provided for the majority of compounds.
http://biocyc.org/open-compounds.shtml

BRaunschweig ENzyme DAtabase"  info
 

BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers.
The development of an enzyme data information system was started in 1987 at the German National Research Centre for Biotechnology in Braunschweig (GBF) and is now continued at the University of Cologne, Institute of Biochemistry.
http://www.brenda-enzymes.info/

Biodegradative Strain Database
 

The Biodegradative Strain Database (BSD) was developed by the Center for Microbial Ecology at Michigan State University and Rutgers University.
http://bsd.cme.msu.edu/

CellPro Database
 

Cellular Properties Database provides a simple repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells.
http://senselab.med.yale.edu/senselab/CellPropDB/default.asp

Chemical Entities of Biological Interest
 

Chemical Entities of Biological Interest (ChEBI) is a database of small molecular entities. The term molecular entity encompasses 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.
http://www.ebi.ac.uk/chebi/

Chemcyclopedia
 

Chemcyclopedia’s encyclopedic coverage of the world’s major chemical products embraces the following principal areas:

  • Organic (aliphatic, aromatic, alicyclic, heterocyclic, hydrocarbon, chiral)
  • Organometallic
  • Inorganic (metallic, non-metallic, rare-earth)
    with many hundreds of Specialty and Fine Chemicals being represented.
    http://www.chemcyc.org/

  • Chemfinder
     

    CHEMFINDER finds ...
    Chemical Structures: 2D structures & 3D models
    Physical Properties: MP, BP, CAS RN, & more
    Hyperlinks: Links to other websites with information about the searched compound
    http://www.chemfinder.com

    CHEMID"  info
     

    ChemIDplus is a free, web-based search system that provides access to structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases. ChemIDplus also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest. The database contains over 400,000 chemical records, of which over 300,000 include chemical structures, and is searchable by Name, Synonym, CAS Registry Number, Molecular Formula, Classification Code, Locator Code, and Structure.
    http://chem.sis.nlm.nih.gov/chemidplus/

    Pathway Interaction Database
     

    This is the preliminary version of a database of pathway interactions, assembled by NCICB staff from publicly available sources of information.
    http://pid.nci.nih.gov/

    Center for Chemical Methodology and Library Development / Synthesis Procols
     

    Synthesis Protocols is a database for solid phase, solution phase and library synthesis procedures currently developed at Boston University's Center for Chemical Methodology and Library Development (CMLD-BU).
    http://cmld.bu.edu/

    Catalytic Site Atlas (CSA)
     

    The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
    http://www.ebi.ac.uk/thornton-srv/databases/CSA/

    Cambridge Structural Database
     

    The world repository of small molecule crystal structures.
    http://www.ccdc.cam.ac.uk/products/csd/

    Comparative Toxicogenomics Database (CTD)"  info
     

    The Comparative Toxicogenomics Database (CTD) identifies interactions between chemicals and genes/proteins in diverse organisms to elucidate the molecular mechanisms by which environmental chemicals affect human health.
    CTD curates chemical-gene/protein interactions from the published literature and integrates diverse data (chemicals, genes/proteins, references, sequences, vertebrate and invertebrate organisms, and Gene Ontology) to facilitate unique cross-species and functional perspectives on toxicogenomic information
    http://ctd.mdibl.org/

    Database of Quantitative Cellular Signaling
     

    The Database of Quantitative Cellular Signaling is a repository of models of signaling pathways.
    http://doqcs.ncbs.res.in/

    Dehydrogenase Enzyme Stereospecificities Database"  info
     

    The Dehydrogenase Stereospecificity Database(DSD) provides a compilation of enzyme stereochemical data.
    http://www.darrenflower.info/DSD/dehydrog.htm

    Encyclopedia of Escherichia coli K12 Genes and Metabolism"  info
     

    The EcoCyc database is a source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli.
    http://ecocyc.org/

    Enzymes and Metabolic Pathways database (EMP)
     

    Enzymes and Metabolic Pathways database, EMP, is a unique and most comprehensive electronic source of biochemical data. It covers all aspects of enzymology and metabolism and represents the whole factual content of original journal publications.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+EMP

    Enzyme (EMBL)
     

    The ENZYME data bank contains the following data for each type of characterized enzyme for which an EC number has been provided: EC number, Recommended name, Alternative names, Catalytic activity, Cofactors, Pointers to the SWISS-PROT entrie(s) that correspond to the enzyme, Pointers to disease(s) associated with a deficiency of the enzyme.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+ENZYME

    Enzyme Nomenclature Database
     

    The ENZYME database is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB), and it contains the following data for each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided:

  • EC number
  • Recommended name
  • Alternative names (if any)
  • Catalytic activity
  • Cofactors (if any)
  • Pointers to the Swiss-Prot protein sequence entrie(s) that correspond to the enzyme (if any)
  • Pointers to human disease(s) associated with a deficiency of the enzyme (if any)
    http://us.expasy.org/enzyme/

  • Enzyme Nomenclature Database
     

    Enzyme Nomenclature. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
    http://www.chem.qmw.ac.uk/iubmb/enzyme/

    ESTerases and alpha / beta Hydrolase Enzymes and Relatives
     

    This server is dedicated to the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases.
    http://bioweb.ensam.inra.fr/ESTHER/general?what=index

    Encyclopedia of Human Genes and Metabolism
     

    HumanCyc is a bioinformatics database that describes the human metabolic pathways and the human genome.
    http://humancyc.org/

    Integrated Relational Enzyme Database
     

    The Integrated relational Enzyme database (IntEnz) will contain enzyme data approved by the Nomenclature Committee. The goal is to create a single relational enzyme database.
    http://www.ebi.ac.uk/intenz/index.html

    iPath
     

    iPath contains interactive maps of biological signaling and metabolic pathways. One can click on select features of the maps for detailed gene and protein information.
    http://escience.invitrogen.com/ipath/

    Chemical Safety Information from Intergovernmental Organizations
     

    IPCS INCHEM is a means of rapid access to internationally peer reviewed information on chemicals commonly used throughout the world, which may also occur as contaminants in the environment and food.
    http://www.inchem.org/

    Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology
     

    Nomenclature database.
    http://www.chem.qmul.ac.uk/iupac

    Glycan Structure Search using KCaM
     

    KCaM is a web service for aligning glycan chains with existing glycan databases.
    http://www.genome.jp/kegg/glycan/

    LIGAND, Database of Chemical Compounds and Reactions in Biological Pathways
     

    LIGAND, Database of Chemical Compounds and Reactions in Biological Pathways, is designed to provide the linkage between chemical and biological aspects of life in the light of enzymatic reactions. The database consists of four sections: COMPOUND, GLYCAN, REACTION, and ENZYME The COMPOUND section is a collection of metabolic and other compounds including substrates, products, inhibitors of metabolic pathways as well as drugs and xenobiotic chemicals. Each of the chemical substances that appear in the REACTION and ENZYME sections and KEGG/PATHWAY database is identified by an accession number and stored in this section. Each entry of COMPOUND contains information of naming, chemical formula, structural formula in a separate GIF file and a MOL file, metabolic and other pathways, related enzymes, related protein structures, prosthetic groups and CAS (Chemical Abstracts Service) registry number.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+LCOMPOUND

    Lipase Engineering Database"  info
     

    The Lipase Engineering Database (LED) integrates information on sequence, structure, and function of lipases, esterases, and related proteins.
    http://www.led.uni-stuttgart.de/

    Mechanism, Annotation and Classification in Enzymes
     

    MACiE, which stands for Mechanism, Annotation and Classification in Enzymes, is a unique database of enzyme reaction mechanisms, focusing on well characterised enzymes with PDB entries and relatively well understood mechanisms. All mechanisms have been taken from the primary literature and curated by a trained chemist and biochemist. MACiE is a collaborative project between the Mitchell Group at the Unilever Centre for Molecular Informatics part of the University of Cambridge and the Thornton Group at the European Bioinformatics Institute.
    http://www.ebi.ac.uk/thornton-srv/databases/MACiE/

    Malaria - Metabolic Pathways
     

    Metabolic pathways of plasmodium falciparum; a database, provided by the Hebrew University of Jerusalem, compiled and maintained by Hagai Ginsburg.
    http://sites.huji.ac.il/malaria/

    The Merck Chemical Databases
     

    The Merck Online Catalog provides basic informations about chemicals.
    http://www.merck-chemicals.com/germany/all-products

    Multiorganism Database of Metabolic Pathways and Enzymes"  info
     

    MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways from more than 300 different organisms.
    http://metacyc.org/

    Nuclide Table
     

    The number of protons in a nucleus is shown on the vertical axis and the number of neutrons is shown on the horizontal axis. Nuclide charts are mostly colored to visualize a particular property and the nuclide boxes contain a brief summary of nuclear properties.
    http://atom.kaeri.re.kr/ton/

    Protein Data Bank"  info
     

    The data afford the 3-dimensional illustration of proteins.
    http://www.rcsb.org/pdb/

    Periodic Table - WebElements
     

    WebElements aims to be a high quality source of chemistry information on the WWW relating to the periodic table.
    http://www.webelements.com/

    NIST Physics Laboratory Holdings by Element
     

    Periodic table, made by the National Institute of Standards and Technology (NIST), interconnected with databases about...

  • Atomic Spectroscopic Data
  • X-Ray and Gamma Ray Data
  • Radiation Dosimetry Data
  • Nuclear Physics Data
  • Condensed Matter Physics Data
    http://www.physics.nist.gov/PhysRefData/Elements/index.html

  • A Protein Phosphatase Information Resource"  info
     

    PhosphaBase is an ontology-driven database resource containing information on the protein phosphatase family. It is the first public resource dedicated to protein phosphatases, which are enzymes that perform dephosphorylation reactions.
    http://bioinf.man.ac.uk/phosphabase/index.html

    Pyridoxal 5'-Phosphate Dependent Enzymes Mutants Database"  info
     

    The PLPMDB database provides access to relevant mutant information on Pyridoxal-5'-phosphate dependent enzymes.
    http://www.studiofmp.com/plpmdb/index.htm

    Predicted and Consensus Interaction Sites in Enzymes"  info
     

    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.
    http://precise.bu.edu/precisedb/

    Predicted and Consensus Interaction Sites in Enzymes"  info
     

    PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.
    http://precise.bu.edu/

    PubChem"  info
     

  • PubChem Substance
    contains over 800,000 chemical samples imported from 14 public sources including ChemIDplus, the Developmental Therapeutics Program at NCI, KEGG, NCBI MMDB, and the NIST Chemistry WebBook.
  • PubChem Compound
    Chemical entities in PubChem Substance records that have known structures are validated, converted to a standardized form, and imported into PubChem Compound. This standardizing allows NCBI to compute chemical parameters and similarity relationships between compounds. The compounds are grouped into levels of chemical similarity from most general to most specific.
  • PubChem BioAssay
    currently contains over 170 bioactivity studies from the Developmental Therapeutics Program at NCI, and each of these studies is linked to records in PubChem Substance. The PubChem Bioassay interface allows users to view substances that meet certain activity and/or chemical criteria, and access the matching records in PubChem Substance or downloaded in several formats.
    http://pubchem.ncbi.nlm.nih.gov

  • Radionuclide Safety Data Sheets
     

    Informations about radionuclides.
    http://web.stanford.edu/dept/EHS/prod/researchlab/radlaser/RSDS.html

    Reactive Oxygen Species and Cell Signaling Pathway
     

    ROSPath is a database for proteins involved in ROS-mediated signaling pathways.
    http://rospath.ewha.ac.kr

    Superdrug Database"  info
     

    SuperDrug is a conformational drug database. It contains approximately 2500 3D-structures of active ingredients of essential marketed drugs.
    http://bioinf.charite.de/superdrug/

    Structure-Function Linkage Database"  info
     

  • SFLD is a database that links evolutionarily related sequences and structures from mechanistically diverse superfamilies of enzymes to their chemical reactions.
  • Correlates conserved active site residues with specific partial reactions that all members of a superfamily perform.
    http://sfld.rbvi.ucsf.edu/

  • Signal Transductions Classification Database"  info
     

    The Signal Transduction Classification Database (STCDB) is a database about to the classification of signal transduction.
    http://bibiserv.techfak.uni-bielefeld.de/stcdb/

    SweetDB"  info
     

    SweetDB, a database made by the German Cancer Research Center, Heidelberg, provides annotated carbohydrate structure and substance information.
    http://www.glycosciences.de/sweetdb/

    Thermodynamics of Enzyme-Catalyzed Reactions
     

    Database about the thermodynamics of encyme-catalyzed reactions, made by Robert N. Goldberg, Yadu B. Tewari and T.N.Bhat, Biotechnology Division, National Institute of Standards and Technology Gaithersburg,
    http://xpdb.nist.gov/enzyme_thermodynamics/

    UENZYME
     

    This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UENZYME

    UIMAGEMAP
     

    UIMAGEMAP contains all the graphic-based pathways in UMBBD.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UIMAGEMAP

    UPATHWAY"  info
     

    This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UPATHWAY

    UREACTION
     

    This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the UM-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.
    The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbMI1Kc4xC+-lib+UREACTION

    Metabolic Reconstructions
     

    The WIT Project attempts to produce metabolic reconstructions for sequenced (or partially sequenced) genomes. A metabolic reconstruction is a model of the metabolism of the organism derived from sequence, biochemical, and phenotypic data. WIT includes a set of over 2900 diagrams depicting metabolic pathways.
    http://www-wit.mcs.anl.gov/wit3/