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Lhasa trusted community KNIME nodes Data processing and metabolism prediction
Dr Samuel Webb samuelwebblhasalimitedorg
Who am I
bull Working within the Research Group at Lhasa Limited
bull Activities include bull Software tool development bull Data mining bull Algorithm development bull Managing Lhasarsquos internal KNIME nodes and build bull Managing Lhasarsquos open source KNIME contribution
What is KNIME
bull Analytics platform
bull Core software open source
bull Software development kit (SDK) makes it easy to develop your own nodes
ldquoOur KNIME Analytics Platform is the leading open solution for data-driven innovation designed for discovering the potential hidden in data mining for fresh insights or predicting new futures Organizations can take their collaboration productivity and performance to the next level with a robust range of commercial extensions to our open source platformrdquo ndash wwwknimeorgabout
KNIME and cheminformatics
bull Large number of downloads for the community plugins
bull Large number of community developers
bull Some examples of node types
bull Chemical engines ChemAxon RDKit CDK and Indigo bull General purpose and algorithms Vernalis Enalos and Lhasa bull Data searches CIR and EMBL-EBI
What does Lhasa use KNIME for
bull Data processing bull Combining datasets find overlap compare activities when
overlap exists join in data where no overlap existshellip bull Monitoring
bull Extracting data from a the database which has been altered identifying review work content
bull (Q)SAR bull Model building clustering algorithm development
applicability domains chemical space investigationhellip
LHASA CONTRIBUTION TO KNIME
Free open source plugins released
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Who am I
bull Working within the Research Group at Lhasa Limited
bull Activities include bull Software tool development bull Data mining bull Algorithm development bull Managing Lhasarsquos internal KNIME nodes and build bull Managing Lhasarsquos open source KNIME contribution
What is KNIME
bull Analytics platform
bull Core software open source
bull Software development kit (SDK) makes it easy to develop your own nodes
ldquoOur KNIME Analytics Platform is the leading open solution for data-driven innovation designed for discovering the potential hidden in data mining for fresh insights or predicting new futures Organizations can take their collaboration productivity and performance to the next level with a robust range of commercial extensions to our open source platformrdquo ndash wwwknimeorgabout
KNIME and cheminformatics
bull Large number of downloads for the community plugins
bull Large number of community developers
bull Some examples of node types
bull Chemical engines ChemAxon RDKit CDK and Indigo bull General purpose and algorithms Vernalis Enalos and Lhasa bull Data searches CIR and EMBL-EBI
What does Lhasa use KNIME for
bull Data processing bull Combining datasets find overlap compare activities when
overlap exists join in data where no overlap existshellip bull Monitoring
bull Extracting data from a the database which has been altered identifying review work content
bull (Q)SAR bull Model building clustering algorithm development
applicability domains chemical space investigationhellip
LHASA CONTRIBUTION TO KNIME
Free open source plugins released
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
What is KNIME
bull Analytics platform
bull Core software open source
bull Software development kit (SDK) makes it easy to develop your own nodes
ldquoOur KNIME Analytics Platform is the leading open solution for data-driven innovation designed for discovering the potential hidden in data mining for fresh insights or predicting new futures Organizations can take their collaboration productivity and performance to the next level with a robust range of commercial extensions to our open source platformrdquo ndash wwwknimeorgabout
KNIME and cheminformatics
bull Large number of downloads for the community plugins
bull Large number of community developers
bull Some examples of node types
bull Chemical engines ChemAxon RDKit CDK and Indigo bull General purpose and algorithms Vernalis Enalos and Lhasa bull Data searches CIR and EMBL-EBI
What does Lhasa use KNIME for
bull Data processing bull Combining datasets find overlap compare activities when
overlap exists join in data where no overlap existshellip bull Monitoring
bull Extracting data from a the database which has been altered identifying review work content
bull (Q)SAR bull Model building clustering algorithm development
applicability domains chemical space investigationhellip
LHASA CONTRIBUTION TO KNIME
Free open source plugins released
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
KNIME and cheminformatics
bull Large number of downloads for the community plugins
bull Large number of community developers
bull Some examples of node types
bull Chemical engines ChemAxon RDKit CDK and Indigo bull General purpose and algorithms Vernalis Enalos and Lhasa bull Data searches CIR and EMBL-EBI
What does Lhasa use KNIME for
bull Data processing bull Combining datasets find overlap compare activities when
overlap exists join in data where no overlap existshellip bull Monitoring
bull Extracting data from a the database which has been altered identifying review work content
bull (Q)SAR bull Model building clustering algorithm development
applicability domains chemical space investigationhellip
LHASA CONTRIBUTION TO KNIME
Free open source plugins released
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
What does Lhasa use KNIME for
bull Data processing bull Combining datasets find overlap compare activities when
overlap exists join in data where no overlap existshellip bull Monitoring
bull Extracting data from a the database which has been altered identifying review work content
bull (Q)SAR bull Model building clustering algorithm development
applicability domains chemical space investigationhellip
LHASA CONTRIBUTION TO KNIME
Free open source plugins released
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
LHASA CONTRIBUTION TO KNIME
Free open source plugins released
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
What have we released
General nodes bull Data manipulation
bull Discretise
bull Model scoring
bull Binary Scorer bull Binned performance bull Result
bull Table manipulation
bull Dumb Joiner (to be deprecated) bull Row Splitter (col+) bull Table to HTML
Metabolism nodes bull SMARTCyp 242
bull Cytochrome P450 site of metabolism predictor
bull Integration of Patrick Rydbergrsquos open source tool
bull WhichCyp 12
bull Prediction of binding to Cytochrome P450 isoform(s)
bull Integration of Patrick Rydbergrsquos open source tool
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Disclaimer
bull These nodes plugins are not Lhasa Limited products
bull Help support for these nodes is provided via bull The KNIME forum httpstechknimeorgforumlhasa-nodes bull knimelhasalimitedorg (preferable to use the KNIME
forum)
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
More information
bull httpstechknimeorglhasa-nodes-for-knime
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Why would you use these nodes
Here we calculate the performance of the Random Forest with Morgan
and MACCS fingerprints
Convert the performance table to
HTML and email
Filter out rows where either model predict
active
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Generic nodes model performance
bull Similar functionality to the Scorer node
bull Calculates various performance metrics for binary classification models
bull Can choose multiple prediction columns
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Generic nodes table to HTML
bull Convert a table to a single HTML cell
bull The String render will render HTML tags
bull Select which columns to include
bull StringValue IntValue DoubleValue
bull Creates a single cell output
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242
bull SMARTCyp is a method for prediction of which sites in a molecule
that are most liable to metabolism by Cytochrome P450
bull It has been shown to be applicable to metabolism by the isoforms
1A2 2A6 2B6 2C8 2C19 2E1 and 3A4 and specific models for
the isoform 2C9 and isoform 2D6 are included in KNIME 242
bull SMARTCyp is Developed by the Department of Drug Design and
Pharmacology at the University of Copenhagen and is funded by
Lhasa Limited More details can be found at
httpwwwfarmakudksmartcypaboutphp
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242 usage
bull Letrsquos recreate the results table from bull httpwwwncbinlmnihgovpmcarticlesPMC4055970 bull SMARTCyp A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism bull Patrik Rydbergdagger David E Gloriamdagger Jed ZaretzkiDagger Curt BrenemanDagger and Lars Olsendagger
bull Metabolic position = any site listed as primary secondary or tertiary bull Use the top 3 predicted sites Accuracy increases as you increase the rank
limit bull When considering only the top ranked site there is a 65 accuracy in
identifying an experimentally seen SOM vs 81 using the top 3 sites
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242 usage
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242 usage
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
SMARTCyp 242 usage
bull Here wersquove incorporated multiple
chemical engines from the same platform
bull RDKit
bull Rendering
bull CDK
bull Rendering bull SMARTCyp processing
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
WhichCyp
bull Predicts binding to Cyp isoforms 1A2 2C9 2C19 2D6 and 3A4
bull Further reading
bull Michal Rostkowski Ola Spjuth and Patrik Rydberg WhichCyp Prediction of Cytochromes P450 Inhibition Bioinformatics 2013 29 2051-2052
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
WhichCyp usage
bull Renders images of the predictions as a PNG
bull May be updated to SVG in the future
bull Input a structure column that is compatible
with a CDK Value such as
bull Mol bull SDF bull Smiles bull CDK
bull Outputs the values you would get in the CSV
file when running manually
bull Binding Missing Signatures and sensitivity warnings
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
WHERE CAN I GET THEM
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Getting our nodes
bull Download KNIME httpswwwknimeorgdownloadsoverview
bull Selecting + all free extensions and Lhasarsquos will be included
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Getting our nodes
bull Alternatively they can be added to an existing KNIME
bull Trusted Community Contributions - httpupdateknimeorgcommunity-contributionstrusted31
Thank you
Support httpstechknimeorgforum
Thank you
Support httpstechknimeorgforum