ChemBank: a small-molecule screening and cheminformatics resource database

By Stefan Schreiber, K. Seiler, Gregory A. George, Gregory A. George, M. P. Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, S. Brudz, John P. Sullivan and 9 more. 2007

280 citations recorded by the source corpus.

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.

Subfields: Biophysics, Computational Theory and Mathematics, Molecular Biology, Computational Chemistry & Drug Discovery

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Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “Database Zinc [175,176] PubChem [177,178] ChemSpider [179,180] ChEMBL [181,182] NuBBE DB [183,184] ChemBank [185,186] eMolecules [187] DrugBank [188,189] Binding DB [190,191] In a following step, the prepared database is docked into the target binding site.”
ChEMBL: a large-scale bioactivity database for drug discovery (2011, background): “PubChem BioAssay (6) and ChemBank (7) are large archival databases providing access to millions of deposited screening results, typically from high-throughput screening (HTS) experiments.”
PubChem: a public information system for analyzing bioactivities of small molecules (2009, background): “ChemBank (12) is a database for biological screening data generated by HTS experiments.”
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “Many public chemical databases, such as PharmGKB (8), DrugBank (9), ChemBank (10) and STITCH (11) focus on drugs and other small molecules, providing an invaluable resource for therapeutic research.”
Virtual screening strategies in drug discovery: a critical review. (2013, background): “They include known drugs, carbohydrates, synthetic, natural and targeted compounds (Table 4) [40-47].”
Review of Drug Repositioning Approaches and Resources (2018, background): “Publicly available databases [9] [79-84] of chemical structures contain massive amounts of useful information such as 2D topological fingerprints and 3D conformations.”
Discovery of drug mode of action and drug repositioning from transcriptional responses (2010, background): “%) drugs from two public repositories, DrugBank (27) and ChemBank (28).”
The BioGRID interaction database: 2017 update (2016, background): “…of the major specialized chemical interaction databases, including DrugBank (37), HMdb (61), T3DB (62), BindingDB (63), CTD (64), Therapeutic Target DB (65), ChemBank (66), PharmGKB (67), DGIdb (68), Pub-Chem (69) and ChEMBL (70) to determine the shared fields housed in each of these databases.”
A side effect resource to capture phenotypic effects of drugs (2010, methodology): “Data on cellular phenotypes in response to chemicals are stored in PubChem BioAssay and ChemBank (Seiler et al , 2008).”
An overview of the PubChem BioAssay resource (2009, background): “It also includes ligand–protein binding activity data generated by the targeted high-throughput structural biology experiments at the European Structural Genomics Consortium (11), literature-extracted bioactivity data from the BindingDB (12) project, the IUPHAR (13) project and the PDBBind (14) proj”