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                -> CHEM1...know the structure and function of anti-inflammatory drugs like aspirin or celebrex ? (last update Aug. 23, 2005) 
                -> CHEM2...know the genes and drugs related to diseases like atherosclerosis ? (last update Aug. 23, 2005)  
              
                           
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CHEM1...know the structure and function of anti-inflammatory drugs like aspirin or celebrex ? (last update Aug. 23, 2005)  
       
    Tip! PubChem is a collection of databases provided by the NCBI, which contains the chemical structures of small organic molecules and information on their biological activities. PubChem is organized as three linked databases within the Entrez/PubMed information retrieval system, meaning that all 3 databases can be searched "in one run". These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides PubChem Structure Search, a fast chemical structure similarity search tool that links to the PubChem Compound and PubChem Substance databases. PubChem is an excellent resource if you want to know more about substances like "aspirin", "gleevec", "simvastatin", or "celebrex".
    PubChem Substance contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. PubChem Substances have a "SID" identifier.
    PubChem Compound contains validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures. PubChem Compounds have a "CID" identifier.
    PubChem BioAssay contains bioactivity screens of chemical substances described in PubChem Substance. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. PubChem BioAssay entries have an "AID" identifier.

    Tip! The NCBI Structure group maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB, the Molecular Modeling Database, contains experimentally determined biopolymer structures obtained from the Protein Data Bank (PDB). 3D structures are easily displayed using the program Cn3D (please see chapter "Visualization Software"). If you want to search the NCBI structure database using keywords, protein or nucleotide sequence, go to Entrez Structure. MMDB can also be used very efficiently if you want to retrieve structures of drugs in complex with their targets. Please refer to the main section of MMDB for details !

    Tip! PharmGKB - the "Pharmacogenetics and Pharmacogenomics Knowledgebase", is a research tool developed by Stanford University with funding from the National Institutes of Health (NIH). Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. The PharmGKB database is a central repository for genetic and clinical information about people who have participated in research studies at various medical centers in the PGRN. In addition, genomic data, molecular and cellular phenotype data, and clinical phenotype data are accepted from the scientific community at large. This means that the scope of PharmGKB is not only to store information on "small molecule entities" but to cross-reference these data also with genes and diseases. Thus, you can search PharmGKB using either a gene name, a drug name (like "aspirin" or "celebrex"), or a disease name. You may also browse all genes, drugs, diseases and even pathways which are listed alphabetically. Taken together, the interface is very user-friendly. In order to see some typical PharmGKB entries, please refer to section PharmGKB IDs.

    Tip! The KEGG LIGAND database is part of the KEGG portal which turns sequence information from a number of organisms into metabolic or regulatory pathways. The KEGG LIGAND database processes requests related to drug names very efficiently, whereas KEGG GENES is used to query by gene names. Tests using disease names were not successful. KEGG LIGAND is a composite database consisting of COMPOUND, GLYCAN, REACTION, RPAIR, and ENZYME databases. ENZYME is derived from the Enzyme Nomenclature, but the other four are developed and maintained at KEGG in a common relational database. You may search for drugs by using the KEGG Compound database via the search field "Name". Note: If available, there are direct links to other compound databases like PubChem and ChEBI. Note: Please refer also to the other resources described in section "Small Molecules Databases" for comparison !
                   
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CHEM2...know the genes and drugs related to diseases like atherosclerosis ? (last update Aug. 23, 2005)  
              
    Tip! PharmGKB - the "Pharmacogenetics and Pharmacogenomics Knowledgebase", is a central repository for genetic and clinical information about people who have participated in research studies at various medical centers in the PGRN. The scope of PharmGKB is not only to store information on "small molecule entities" but to cross-reference these data also with genes and diseases. Thus, you can search PharmGKB using either a gene name, a drug name, or a disease name (like "atherosclerosis"). This will retrieve related gene reports, like APOE and ACE, as well as drug reports, like simvastatin and fluvastatin. The latter will then also link to the PharmGKB Pathway database, in this case to the Statin pathway. In general, please also refer to FAQ CHEM1.

    PubChem is a collection of databases provided by the NCBI, which contains the chemical structures of small organic molecules and information on their biological activities. PubChem is organized as three linked databases within the Entrez/PubMed information retrieval system, meaning that all 3 databases can be searched "in one run". These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem may also be queried using disease names. A test showed that all 3 test disease names (Atherosclerosis, Alzheimer, Inflammation) are found. Note: A drug-disease correlation is only found in cases where the disease name is mentioned in the section "Medical Subject Annotations" of a PubChem entry. This produces only a few hits with "atherosclerosis" and "alzheimer" but a long list of hits with "inflammation". Note: Please refer also to the other resources described in section "Small Molecules Databases" for comparison !

    MMDB, a database of macromolecular 3D structures, maintained by the NCBI (see CHEM1), can also be used to query for structures of proteins and drugs related to specific diseases. A test using 3 test disease names (Atherosclerosis, Alzheimer, Inflammation) showed that all are found in Entrez Structure, displaying lists of protein / drug structures related to the diseases. Nevertheless, it should be mentioned that probably only a fraction of the disease-related molecules can be retrieved via this strategy. Please refer also to the main section of MMDB for details !  
                       
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