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ToxChallenge_​ER_​LBD_​pred_​1

TARGET Input:Training Set Input:external actives Input:Compounds to be predictedFingerprints of the training set:csv file containing fingerprints as well as activities file format: ;-seperated filefirst column: compound name, followed by target activity columns named AR, AR_LBD,AHR, ER, ER_LBD, AROMATASE,PPAR_GAMMA, ARE, ATAD5, HSE,MMP and P53 and containing thevalues 0 (inactive), 1 (active) andnull (inconclusive);followed by columns of thefingerprinttraining: inactivesTARGET definedas ER_LBDactivities 0 or 1,remove inconclusivecalculate correlationbetween featuresfilter out featureswith high correlationbit vector -filtered fingerprintfeaturesremove unnecessarycolumnstraining: activesExternal set fingerprints in case external activesfrom the ChEMBL databaseare used; include onlycompounds with specifiedactivity values (e.g. <5 µM);same file format as abovebit vector - filteredfingerprint featureskeep activesfor specified targetTARGET: ER_LBDremove unnecessary columnsgroup by name= remove duplicatesAdd external or not?actives + externpick most diverse activesinactives + diverse activesNaive Bayes modelZ-score T max: activesT avg: activesT max: inactivesT2 = 1 - T2(Tanimoto similarityto inactives) Combine Bayes scores B0 = 1 - B0(Bayes score for inactivity)Combine TanimotoscoresMin-MaxConsensus scoreBayes + Tanimotofilter out featureswith high correlationin training setwrite prediction fileremove unnecessarycommentsFingerprints of compounds to be predictedfilter out featureswith high correlationin training setbit vector - filteredfingerprint featuresremove unnecessary columnsrename scorerename compound nameACTIVITY_VALUECSV Reader Row Filter Column Rename Row Filter Linear Correlation Correlation Filter Create Bit Vector Column Filter Row Filter CSV Reader Create Bit Vector Row Filter Column Rename Column Filter GroupBy Column Rename Row Filter Concatenate RDKit DiversityPicker Concatenate FingerprintBayesian Learner FingerprintBayesian Predictor Normalizer FingerprintSimilarity FingerprintSimilarity FingerprintSimilarity Math Formula Column Aggregator Math Formula Column Aggregator Normalizer Column Aggregator Correlation Filter CSV Writer Column Filter CSV Reader Correlation Filter Create Bit Vector Column Filter Column Rename String Manipulation Column Rename TARGET Input:Training Set Input:external actives Input:Compounds to be predictedFingerprints of the training set:csv file containing fingerprints as well as activities file format: ;-seperated filefirst column: compound name, followed by target activity columns named AR, AR_LBD,AHR, ER, ER_LBD, AROMATASE,PPAR_GAMMA, ARE, ATAD5, HSE,MMP and P53 and containing thevalues 0 (inactive), 1 (active) andnull (inconclusive);followed by columns of thefingerprinttraining: inactivesTARGET definedas ER_LBDactivities 0 or 1,remove inconclusivecalculate correlationbetween featuresfilter out featureswith high correlationbit vector -filtered fingerprintfeaturesremove unnecessarycolumnstraining: activesExternal set fingerprints in case external activesfrom the ChEMBL databaseare used; include onlycompounds with specifiedactivity values (e.g. <5 µM);same file format as abovebit vector - filteredfingerprint featureskeep activesfor specified targetTARGET: ER_LBDremove unnecessary columnsgroup by name= remove duplicatesAdd external or not?actives + externpick most diverse activesinactives + diverse activesNaive Bayes modelZ-score T max: activesT avg: activesT max: inactivesT2 = 1 - T2(Tanimoto similarityto inactives) Combine Bayes scores B0 = 1 - B0(Bayes score for inactivity)Combine TanimotoscoresMin-MaxConsensus scoreBayes + Tanimotofilter out featureswith high correlationin training setwrite prediction fileremove unnecessarycommentsFingerprints of compounds to be predictedfilter out featureswith high correlationin training setbit vector - filteredfingerprint featuresremove unnecessary columnsrename scorerename compound nameACTIVITY_VALUECSV Reader Row Filter Column Rename Row Filter Linear Correlation Correlation Filter Create Bit Vector Column Filter Row Filter CSV Reader Create Bit Vector Row Filter Column Rename Column Filter GroupBy Column Rename Row Filter Concatenate RDKit DiversityPicker Concatenate FingerprintBayesian Learner FingerprintBayesian Predictor Normalizer FingerprintSimilarity FingerprintSimilarity FingerprintSimilarity Math Formula Column Aggregator Math Formula Column Aggregator Normalizer Column Aggregator Correlation Filter CSV Writer Column Filter CSV Reader Correlation Filter Create Bit Vector Column Filter Column Rename String Manipulation Column Rename

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Created by: gosia
Created at: 2014-11-10
On NodePit since: 2024-12-26
Last update: 2025-01-22
Created with KNIME version: v2.11.2.0046103

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