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WCAIR_​isosteric_​replacement_​suggestions_​table_​builder

<p>This workflow was created to curate and format lists of isosteric replacements. It creates two databases: a normal and an expanded version of it, containing pairs of isosteric replacements that can be applied to a scaffold molecule (this will be applied a separate workflow).</p><p></p><p>The workflow exports the table in two formats: KNIME's internal .table format, and as a tab-separated CSV.</p><p></p><p>You can see this workflow's result CSV table in action as a Jupyter Notebook: https://github.com/cedricgr/isosteric-replacements</p><p></p>

URL: Bioisostere (Wikipedia) https://en.wikipedia.org/wiki/Bioisostere
URL: Bioisosterism:  A Rational Approach in Drug Design https://pubs.acs.org/doi/10.1021/cr950066q
URL: Isosteric Replacements exercise (Jupyter Notebbok) https://github.com/cedricgr/isosteric-replacements

Phenyl ring bioisosteresfrom DOI 10.1021/acs.jmedchem.1c01215
Table Creator
Reads the isosteresubstitution table from Ertl, P. - DOI 10.1021/acs.jcim.0c00290
CSV Reader
Changes column A -> B and vice-versaif B is isostere of A, so A is of Bthanks to Dr. Peter Ertl for the suggestion
Column Resorter
Removes rows in whichA -> A exchange is proposed
Rule-based Row Filter
If A and B are isosteres of C, that meansthat A and B are isosteres toogroups rows with the same reference
Joiner
Concatenate
Column Renamer
Stacks the tables togetherresets RowID
Concatenate
Column Renamer
Generates the RegExDictionary table to fixSMILES errors and ringdescriptions
Table Creator
Duplicate Row Filter
Fixes SMILES errorsFixes rings descriptionschanges [R] to [*][RX] to [*:X]
String Replacer (Dictionary)
There may be items fromoriginal table that are missingin the join operation
Concatenate
Adjust SMARTS queriesbuild SMARTS reaction column
Table processng
Writes the table on disk usingKNIME's built-in .table formatfor the isosteric replacementsworkflow
Table Writer
Phenol bioisosteresfrom 10.1002/ardp.202400700
Table Creator
Export as tab-delimited valuesfor Jupyter Notebook
CSV Writer
Duplicate Row Filter
Constant Value Column
Adjust SMARTS queriesbuild SMARTS reaction column
Table processng
Export as tab-delimited valuesfor Jupyter Notebook
CSV Writer
Amide bioisosteresfrom 10.1021/acs.jmedchem.0c00530
Table Creator
Writes the table on disk usingKNIME's built-in .table formatfor the isosteric replacementsworkflow
Table Writer

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