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ChemBank: a small-molecule screening and cheminformatics resource database.

Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA - Nucleic Acids Res. (2007)

Bottom Line: ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules.Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied.The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

View Article: PubMed Central - PubMed

Affiliation: Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.

ABSTRACT
ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

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ChemBank offers multiple routes to find chemical information. Search tools allowing structure drawing (28) for substructure or similarity searches (a), selection of calculated molecular descriptors (b) and selection of term-based bioactivity annotations (c), each provide avenues to find individual molecules or sets of molecules in ChemBank. The ChemBank ‘Molecule Display’ webpage (background) provides detailed information about each molecule, including structure, names, molecular descriptors, biological annotations, sample information and screening instances.
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Figure 2: ChemBank offers multiple routes to find chemical information. Search tools allowing structure drawing (28) for substructure or similarity searches (a), selection of calculated molecular descriptors (b) and selection of term-based bioactivity annotations (c), each provide avenues to find individual molecules or sets of molecules in ChemBank. The ChemBank ‘Molecule Display’ webpage (background) provides detailed information about each molecule, including structure, names, molecular descriptors, biological annotations, sample information and screening instances.

Mentions: ChemBank has multiple search interfaces available to the user to enable both simple and complex queries. Users can search for small molecules using properties such as presence of a substructure (Figure 2a), calculated molecular descriptors (Figure 2b) or association with a curated biological activity (Figure 2c). Results from such searches lead the user to a ‘Molecule Display’ view, which shows basic information about the small molecule, including names, structure, chemical descriptors, biological activity and screening test instances (Figure 2, background).Figure 2.


ChemBank: a small-molecule screening and cheminformatics resource database.

Seiler KP, George GA, Happ MP, Bodycombe NE, Carrinski HA, Norton S, Brudz S, Sullivan JP, Muhlich J, Serrano M, Ferraiolo P, Tolliday NJ, Schreiber SL, Clemons PA - Nucleic Acids Res. (2007)

ChemBank offers multiple routes to find chemical information. Search tools allowing structure drawing (28) for substructure or similarity searches (a), selection of calculated molecular descriptors (b) and selection of term-based bioactivity annotations (c), each provide avenues to find individual molecules or sets of molecules in ChemBank. The ChemBank ‘Molecule Display’ webpage (background) provides detailed information about each molecule, including structure, names, molecular descriptors, biological annotations, sample information and screening instances.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238881&req=5

Figure 2: ChemBank offers multiple routes to find chemical information. Search tools allowing structure drawing (28) for substructure or similarity searches (a), selection of calculated molecular descriptors (b) and selection of term-based bioactivity annotations (c), each provide avenues to find individual molecules or sets of molecules in ChemBank. The ChemBank ‘Molecule Display’ webpage (background) provides detailed information about each molecule, including structure, names, molecular descriptors, biological annotations, sample information and screening instances.
Mentions: ChemBank has multiple search interfaces available to the user to enable both simple and complex queries. Users can search for small molecules using properties such as presence of a substructure (Figure 2a), calculated molecular descriptors (Figure 2b) or association with a curated biological activity (Figure 2c). Results from such searches lead the user to a ‘Molecule Display’ view, which shows basic information about the small molecule, including names, structure, chemical descriptors, biological activity and screening test instances (Figure 2, background).Figure 2.

Bottom Line: ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules.Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied.The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

View Article: PubMed Central - PubMed

Affiliation: Chemical Biology Program and Platform, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA.

ABSTRACT
ChemBank (http://chembank.broad.harvard.edu/) is a public, web-based informatics environment developed through a collaboration between the Chemical Biology Program and Platform at the Broad Institute of Harvard and MIT. This knowledge environment includes freely available data derived from small molecules and small-molecule screens and resources for studying these data. ChemBank is unique among small-molecule databases in its dedication to the storage of raw screening data, its rigorous definition of screening experiments in terms of statistical hypothesis testing, and its metadata-based organization of screening experiments into projects involving collections of related assays. ChemBank stores an increasingly varied set of measurements derived from cells and other biological assay systems treated with small molecules. Analysis tools are available and are continuously being developed that allow the relationships between small molecules, cell measurements, and cell states to be studied. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the Broad Institute by collaborators from the worldwide research community. The goal of ChemBank is to provide life scientists unfettered access to biomedically relevant data and tools heretofore available primarily in the private sector.

Show MeSH