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Pack KNIME workflows from Zdrazil et al, MedChemComm, 201...


Created: 2016-07-20 06:21:03 | Last updated: 2017-06-22 13:35:07

Included are 2 KNIME workflows for data retrieval and processing:1) a KNIME workflow called "Transporter_Profiling_SERT_DAT_HERGlabel" with HERG labels included2) a KNIME workflow called "Transporter_Profiling_SERT_DAT_Ki_IC50_tailored_TH" without HERG labels

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Pack Workflows for scaffold trend analyses


Created: 2017-06-22 13:01:47 | Last updated: 2018-06-14 09:37:37

These two KNIME workflows were used to process the raw data (retrieved via sql query from ChEMBL) in order to retrieve the final data for scaffold trend analyses as described in the paper: "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. Guha, Journal of Medicinal Chemistry, 2018, 61 (11), pp 4688-4703.

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Workflows (5)

Workflow KNIME workflow used to collate data for th... (1)

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KNIME workflow used to collate data from different sources (Open Data, in-house data) for certain protein targets of interest; further the data is filtered for certain activity endpoints, erraneous data is removed and data overlap between the different sources as well as the targets under study is determined and given as an output;Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community...

Created: 2015-11-02 | Last updated: 2016-03-29

Credits: User Barbara Zdrazil User Daniela Digles Network-member Open PHACTS

Workflow KNIME workflow with hERG labels included f... (1)

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KNIME workflow used to retrieve and process data from Open PHACTS for three targets of interest (hSERT, hDAT, hERG). Further, Murcko scaffolds are computed and selectivity trends towards hSERT and hDAT can be studied. Compounds/scaffold series are flagged by their ability to also inhibit hERG.Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community Contributions (2.11)': EMBL-EBI No...

Created: 2016-07-20 | Last updated: 2016-07-20

Credits: Network-member Open PHACTS

Workflow KNIME workflow without hERG labels include... (1)

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KNIME workflow used to retrieve and process data from Open PHACTS for three targets of interest (hSERT, hDAT, hERG). Further, Murcko scaffolds are computed and selectivity trends towards hSERT and hDAT can be studied. Cutt off's for separating actives/inactives are tailored to the specific target and endpoint.Requirements:- Knime v2.11- Open PHACTS Knime nodes version 1.1.0: https://github.com/openphacts/OPS-Knime- KNIME additional community nodes: 'Trusted Community Contributions (2....

Created: 2016-07-20 | Last updated: 2016-07-20

Credits: User Barbara Zdrazil Network-member Open PHACTS

Workflow Scaffolds_trends_workflow_1 (1)

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First part of the workflow for paper "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. GuhaIncludes initial filtering steps, extraction of Murcko frameworks, inclusion of journal Impact Factors, and calculation of Z-Scores. The example of oxetane substructure search is also included.

Created: 2017-06-22 | Last updated: 2017-06-22

Credits: User Barbara Zdrazil

Workflow Scaffolds_trends_workflow_2 (1)

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Second part of the workflow for paper "The rise and fall of a scaffold: A trend analysis of scaffolds in the medicinal chemistry literature" by B. Zdrazil and R. GuhaIncludes grouping and filtering steps to retrieve the summary data needed for performing the scaffold trend, bioactivity, and liability analyses.

Created: 2017-06-22

Credits: User Barbara Zdrazil

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Non-Information Resource URI: http://www.myexperiment.org/tags/4522


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