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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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Illustration of ChemBank visualizations and linking activities with chemical information. Screening data, including raw measurements, in ChemBank are addressable by exact plate and well position in assay plates (a), and statistical data representing outcomes (b) can be reviewed at the level of raw or normalized data. A multi-assay analysis capability takes advantage of the standard analysis procedure (Figure 4) to display the performance of such similar compounds in multiple assays to which each has been exposed (c). Each of these capabilities can be combined with structure and annotation-based search capabilities to provide cheminformatic analysis of molecules scoring as ‘hits’ in biological assays (d).
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Figure 5: Illustration of ChemBank visualizations and linking activities with chemical information. Screening data, including raw measurements, in ChemBank are addressable by exact plate and well position in assay plates (a), and statistical data representing outcomes (b) can be reviewed at the level of raw or normalized data. A multi-assay analysis capability takes advantage of the standard analysis procedure (Figure 4) to display the performance of such similar compounds in multiple assays to which each has been exposed (c). Each of these capabilities can be combined with structure and annotation-based search capabilities to provide cheminformatic analysis of molecules scoring as ‘hits’ in biological assays (d).

Mentions: Currently, there are four available screening data visualizations in ChemBank. A simple heatmap visualization for assay plates corresponds to the microplate layout in a screening experiment (Figure 5a). For statistical analysis of results from multiple assay plates comprising a single HTS experiment, ChemBank offers both histogram (Figure 5b) and scatterplot (Figure 4e) views. Finally, multi-assay visualization is possible via the ‘Feature Visualization’ webpage (Figure 5c) which is generated by implementation of the standard analysis model to provide a heatmap representing ChemBank ‘Composite Z-score’ values for a series of assays and compounds. These visualization tools can be used in conjunction with the structure similarity, substructure matching, and molecular descriptor filtering capabilities described previously to perform structure–activity relationship analyses (Figure 5d). Taken together, these search and visualization tools represent an implementation of chemical-genetic profiling and cheminformatic analysis capabilities within ChemBank.Figure 5.


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)

Illustration of ChemBank visualizations and linking activities with chemical information. Screening data, including raw measurements, in ChemBank are addressable by exact plate and well position in assay plates (a), and statistical data representing outcomes (b) can be reviewed at the level of raw or normalized data. A multi-assay analysis capability takes advantage of the standard analysis procedure (Figure 4) to display the performance of such similar compounds in multiple assays to which each has been exposed (c). Each of these capabilities can be combined with structure and annotation-based search capabilities to provide cheminformatic analysis of molecules scoring as ‘hits’ in biological assays (d).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Illustration of ChemBank visualizations and linking activities with chemical information. Screening data, including raw measurements, in ChemBank are addressable by exact plate and well position in assay plates (a), and statistical data representing outcomes (b) can be reviewed at the level of raw or normalized data. A multi-assay analysis capability takes advantage of the standard analysis procedure (Figure 4) to display the performance of such similar compounds in multiple assays to which each has been exposed (c). Each of these capabilities can be combined with structure and annotation-based search capabilities to provide cheminformatic analysis of molecules scoring as ‘hits’ in biological assays (d).
Mentions: Currently, there are four available screening data visualizations in ChemBank. A simple heatmap visualization for assay plates corresponds to the microplate layout in a screening experiment (Figure 5a). For statistical analysis of results from multiple assay plates comprising a single HTS experiment, ChemBank offers both histogram (Figure 5b) and scatterplot (Figure 4e) views. Finally, multi-assay visualization is possible via the ‘Feature Visualization’ webpage (Figure 5c) which is generated by implementation of the standard analysis model to provide a heatmap representing ChemBank ‘Composite Z-score’ values for a series of assays and compounds. These visualization tools can be used in conjunction with the structure similarity, substructure matching, and molecular descriptor filtering capabilities described previously to perform structure–activity relationship analyses (Figure 5d). Taken together, these search and visualization tools represent an implementation of chemical-genetic profiling and cheminformatic analysis capabilities within ChemBank.Figure 5.

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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