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# Chemical Checker
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The Chemical Checker (CC) is a data-driven resource of small-molecule bioactivity data. The Chemical Checker organizes all the publicly-available bioactivity data as a .
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The Chemical Checker (CC) is a data-driven resource of small molecule bioactivity data. The main goal of the CC is to express data in a format that can be used off-the-shelf in daily computational drug discovery tasks. The resource is organized in five levels of increasing complexity, ranging from the chemical properties of the compounds to their clinical outcomes. In between, we consider targets, off-targets, perturbed biological networks and several cell-based assays, including gene expression, growth inhibition and morphological profiles. The CC is different to other integrative compounds database in almost every aspect. The classical, relational representation of the data is surpassed here by less explicit, machine-learning oriented abstractions of the data (see the CC [Manifesto](manifesto)).
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The CC was first released to the scientific community in the following paper: [Duran-Frigola et al., *Expanding the small molecule similarity principle to all levels of biology* (2019)](https://www.dropbox.com/s/x2rqszfdfpqdqdy/duranfrigola_etal_ms_current.pdf?dl=0)
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The CC is an ever-growing resource maintained by the [Structural Bioinformatics & Network Biology Laboratory](http://sbnb.irbbarcelona.org) at the Institute for Research in Biomedicine [IRB Barcelona](http://irbbarcelona.org). Should you have any inquiries, please send an email to [miquel.duran@irbbarcelona.org](miquel.duran@irbbarcelona.org).
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## Data
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The CC was first released to the scientific community in the following paper: [Duran-Frigola et al., *Expanding the small molecule similarity principle to all levels of biology* (2019)](https://www.dropbox.com/s/x2rqszfdfpqdqdy/duranfrigola_etal_ms_current.pdf?dl=0), and has since produced a number of [related publications](publications).
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The CC is a data-driven resource, thus it contains
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## Source data and datasets
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* [Bioactivity data](data)
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The CC capitalizes on publicly-available bioactivity data fetched from different sources. We are commited to updating the CC resource **every 6 months**.
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For further information, please refer to:
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* [Bioactivity data sources](data)
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* [Chemical libraries](libraries)
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* [Meta-data](database)
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* [File-system organiztion](datasets)
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## Datasets
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## Signaturization of the data
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[Datasets](datasets)
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## Signaturization of the data
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[Signaturization](signaturization)
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For further information, please refer to:
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* [Signaturization](signaturization)
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## Similarity searches in the web
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Similarity searches can be performed at a high level using the CC resource, available at [http://chemicalchecker.org](http://chemicalchecker.org).
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Similarity searches can be performed at a high level using the CC resource, available at [http://chemicalchecker.org](http://chemicalchecker.org). This resource is limited to the 25 *exemplar* datasets of the CC.
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In the *Main* page, the user can query small molecules and obtain an overview of their location inside the CC. The user will learn the CC datasets where these molecules have data available, with gray 2D density plots indicating whether they are peripheral (low-density regions) or central (high-density regions). To have a better sense of the location of query molecules, landmark compounds from popular collections can be displayed. Deeper insights can be obtained by clicking on the *Explore* button for a molecule of choice.
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In the *Explore* page, we look for similar molecules in the CC database and display them in a 25-column table, corresponding to all CC datasets. In CC datasets where the molecule *is* present, we measure similarities to other molecules in the dataset. If the molecule *is not* present, we infer similarities only to the molecules in the dataset.
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For further information, please refer to:
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* [Short web-tutorial](http://chemicalchecker.org/help/)
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* [Statistics](http://chemicalchecker.org/stats/)
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## Customary drug discovery tasks
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The best potential of the CC is to apply it to drug discovery tasks
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For further information, please refer to:
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* [Library characterization](XXX)
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* Target prediction using [TargetMate](XXX)
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* [DeepChem integration](XXX)
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## Connectivity
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[Connectivity](data)
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## Examples
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[Examples](examples) |
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\ No newline at end of file |
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[Connectivity](connectivity) |