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Showing 55 results. Use the filters on the left and the search box below to refine the results.
Type: KNIME Licence: by-sa
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Workflow Genetic Algorithms for BIOISOSTERIC Struct... (1)

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Genetic algorithm workflow to generate novel structures by recombination and mutation and that uses an ML model as a fitness function. Both the fitness function and the fingerprints modified in the model should be the same. ML model cannot have any descriptors other than given fingerprint.Reverse molecular mapping/generation is not part of this workflow and can be done by creating a large Structure-FP database.

Created: 2018-11-06

Credits: User Insilicoconsulting

Workflow Substructure querying | R-group decomposit... (1)

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This workflow creates maximum common substructure (MCS) out of the provided structures and then substructure mining using MCS as a structural query is performed. Obtained hits are then subjected to R-group decomposition to explore their functional groups. Optionally, physicochemical descriptors for individual functional groups can be calculated.

Created: 2018-10-25

Credits: User Alzbeta Tuerkova User Barbara Zdrazil

Workflow Scaffold Analysis | Statistical analysis o... (1)

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This workflow performs an extraction and statistical analysis of Murcko scaffolds for compounds being active against (a) different target(s). Specifically, target-wise detection of Murcko Scaffolds in active versus inactive compounds, filtering steps by removing too generic scaffold (i.e., number of rings equals to one OR number of heteroatoms in a ring is zero or one), calculating the frequency of a particular scaffold which appears frequently in the active over inactive class, applying Fish...

Created: 2018-10-25

Credits: User Alzbeta Tuerkova 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

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 TRPV1 Bioactivity from ChEMBLdb13 and ChEM... (1)

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This workflow allows to extract bioactivity data stored in ChEMBLdb for human TRPV1. Ensure you have installed Chembl and RDKit extensions to run the workflow.

Created: 2016-07-27 | Last updated: 2016-07-27

Credits: User Daria Goldmann

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 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 Phenotypic screening annotation: protocol 6 (1)

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This workflow contains protocol 6 as published in Digles et al., Open PHACTS Computational Protocols for in silico Target validation of Cellular Phenotypic Screens: Knowing the Knowns, MedChemComm, submitted.This workflow requires the Open PHACTS KNIME nodes (org.openphacts.utils.json_1.1.0.zip) available from https://github.com/openphacts/OPS-Knime and the IUPHAR/BPS Guide to Pharmacology data file available from http://guidetopharmacology.org/DATA/interactions.csv.The workflow returns targe...

Created: 2016-05-06

Credits: User Daniela Digles Network-member Open PHACTS

Workflow Phenotypic screening annotation: protocol 5 (1)

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This workflow contains protocol 5 as published in Digles et al., Open PHACTS Computational Protocols for in silico Target validation of Cellular Phenotypic Screens: Knowing the Knowns, MedChemComm, submitted.This workflow requires the Open PHACTS KNIME nodes (org.openphacts.utils.json_1.1.0.zip) available from https://github.com/openphacts/OPS-Knime.This workflow shows compounds which are found both in an assay of interest (upper part of the workflow) and in kinase assays (lower part of the w...

Created: 2016-05-06

Credits: User Daniela Digles Network-member Open PHACTS

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