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    Chem Bank

    Uploaded by

    Karthik Parameswaran

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd

    Chem Bank

    Uploaded by

    Karthik Parameswaran
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    0 views2 pages

    Chem Bank

    Uploaded by

    Karthik Parameswaran

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    You are on page 1of 2

    ChemBank

    ChemBank is a public, web-based database and analysis environment developed through


    collaboration between the Chemical Biology Program at the Broad Institute of Harvard and MIT. It
    serves as a comprehensive resource for small-molecule screening and cheminformatics, facilitating
    the exploration of chemical and biological data across various assays.

    Key Features

     Data Repository: ChemBank houses over 1.2 million unique small-molecule structures and
    contains extensive datasets from more than 2500 high-throughput biological
    assays across 188 screening projects

     Molecular Descriptors: Users can access over 300 calculated molecular descriptors for each
    compound, enhancing the ability to analyze chemical properties

     Raw Screening Data: Unlike many other databases, ChemBank uniquely stores raw
    experimental results, allowing for detailed analysis and validation of screening experiments

     User-Friendly Interfaces: The platform provides multiple search interfaces that enable users
    to conduct both simple and complex queries based on various chemical properties and
    biological activitiesApplications

     High-Throughput Screening (HTS): ChemBank supports researchers in conducting HTS by


    providing tools for data visualization and analysis, such as plate-map visualizations,
    histograms, and scatterplots

     Chemical Genetics Research: The database facilitates research in chemical genetics by


    enabling the study of small molecules' effects on biological systems, thus accelerating drug
    discovery processes

     Cross-Disciplinary Collaboration: ChemBank fosters collaboration among chemists,


    biologists, and computational scientists by providing a centralized platform for sharing data
    and findings related to small molecules and their biological impacts

    ChemBank stands out as a vital resource for researchers in the fields of chemistry and biology. Its
    combination of extensive data storage, advanced analysis tools, and commitment to raw data
    accessibility makes it an invaluable asset for advancing drug discovery and chemical biology
    research.

    Types of Metadata in ChemBank

    1. Compound Information:

     Chemical Structures: Details about over 1.2 million unique small-molecule


    structures.

     Names/Synonyms: Includes IUPAC names and manually curated synonyms for clarity
    and consistency.

    2. Molecular Descriptors:
     Calculated Properties: More than 300 molecular descriptors are calculated for each
    compound, aiding in the analysis of chemical properties.

    3. Assay Metadata:

     Experimental Design: Information about the screening experiments, including assay


    types (e.g., high-throughput screening) and conditions.

     Field-Based Metadata: Collected using controlled vocabularies to standardize terms


    related to assays, enhancing the comparability of data across different experiments

    4. Biological Findings:

     Activity Annotations: Human-curated biological information regarding small


    molecule activities, including links to relevant literature and databases like Entrez
    Gene and PubMed.

    5. Ontological Associations:

     Biological Context: Metadata linking compounds to biological pathways, target


    proteins, cell lines, and species involved in the assays (over 1000 proteins, 500 cell
    lines, and 70 species)

    6. User Information:

     Data on user interactions and contributions to the database, which helps in tracking
    usage patterns and enhancing user experience.

    7. Screening Project Organization:

     Assays are organized hierarchically into screening projects, allowing users to navigate
    related experiments easily.

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