Workflows

Use Case B, KNIME workflow (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, PLoS One. 2014 Dec 18; 9(12):e115460. PMID: 25522365; authored by Joseline Ratnam, Barbara Zdrazil, Daniela Digles, Cuadrado-Rodriguez E, et al. This workflow can be used to retrieve data and perform the analysis described in use case BRequirements:- Knime v2.9- Open PHACTS Knime nodes version 1.0.0 (DON'...

Created: 2014-11-20 | Last updated: 2015-11-03

Credits: Barbara Zdrazil Emiliano Cuadrado Daniela Digles Lars Richter Open PHACTS

Deriving factual information from WHO COVI... (1)

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 WHO has posted a CSV that's frequently updated with COVID abstracts. A simple PubMed search reveals thousands of abstracts too. So here's an NLP pipeline to mine these and extract meaningful sentences/facts using Stanford Open Information Extractor and Biological entity tagging. #knime #naturallanguageprocessing #textanalytics #textmining #covid19 #nlp #datascience #WHO 

Created: 2020-04-12

Credits: Insilicoconsulting

Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: Insilicoconsulting

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: Insilicoconsulting

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: Barbara Zdrazil

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: Barbara Zdrazil

SAR by Rgroup decomposition (1)

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This workflow showcases a simple way to use Rgroup decomposition for SAR analysis.Once R-groups are obtained for several sites on the Scaffold, molecular properties like logP, TPSA, number of heavy/hetero-atoms, various kinds of ring counts are calculated.While medicinal chemistry purists may decry calculating properties for fragments/R-groups, correlating these at each site with Ki (or activity) shows up interesting trends.It's immediately apparent if increasing logP at a given site incr...

Created: 2015-09-15

Credits: Insilicoconsulting

Exploratory Analytics (Time series forecas... (1)

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Created: 2019-03-23

Credits: Georgios Kargas