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Chemistry
Life Sciences Education Bit Vector Distances Hierarchical Clustering Interactive Selection Interactive View Molecule Descriptors Life science I/O Community Nodes
+7
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    Node / Manipulator
    Molecule Type Cast
    Chemistry Translators Streamable
    Node that converts all cells of a chosen string column into several one of several molecule types, such as Mol2, PDB, SDF, CML, H…
    2
    knime
  2. Go to item
    Workflow
    01_Chemistry_basics
    Chemistry Interactive View Life Sciences
    +1
    This workflow demonstrates basic cheminformatics functionality within KNIME Analytics Platform: Reading and writing various chemi…
    knime > Life Sciences > Events > 2021_09_13_Vienna_Summer_School > Beginners > exercises > 01_Interactive_visualization
    1
    knime
  3. Go to item
    Workflow
    Structure standardisation for molecules
    Cheminformatics Standardisation Structure standardisation
    +1
    This workflow uses RDKit to standardise the input structures. The user can use SDF or SMILES structures and standardise them with…
    jenniferh > Public > Structure_standardisation_RDKit
    1
    jenniferh
  4. Go to item
    Workflow
    01_Chemistry_basics
    Chemistry Interactive View Life Sciences
    +1
    This workflow demonstrates basic cheminformatics functionality within KNIME Analytics Platform: Reading and writing various chemi…
    knime > Education > Courses > L4-CH Introduction to Working with Chemical Data > exercises > 01_Chemistry_basics
    1
    knime
  5. Go to item
    Workflow
    Model Selection with Integrated Deployment
    Chemistry Naive bayes Random forest
    +11
    This workflow deploys an advanced parameter optimzation protocol with four machine learning methods. In this implementation the c…
    knime > Life Sciences > Events > 2020_10_Integrated_Deployment_In_Action_Webinar > Model Selection with Integrated Deployment
    1
    knime
  6. Go to item
    Workflow
    01_Chemistry_basics
    Chemistry Interactive View Life Sciences
    +1
    This workflow demonstrates basic cheminformatics functionality within KNIME Analytics Platform: Reading and writing various chemi…
    urbanl > Public > 01_Chemistry_basics
    0
    urbanl
  7. Go to item
    Workflow
    03_Clustering
    Chemistry Hierarchical Clustering Bit Vector Distances
    +4
    This exercise shows how to perform hierarchical clustering using molecule fingerprints and create an interactive view to pick int…
    knime > Life Sciences > Events > 2021_09_13_Vienna_Summer_School > Advanced > exercises > 01_Clustering_Fingerprint_Similarity
    0
    knime
  8. Go to item
    Workflow
    04_SimilaritySearch
    Chemistry Life Sciences Similarity Search
    +2
    In this exercise we expand our results by finding building blocks similar to those we selected in the previous exercise (03_Clust…
    knime > Life Sciences > Events > 2021_09_13_Vienna_Summer_School > Advanced > exercises > 02_SimilaritySearch
    0
    knime
  9. Go to item
    Workflow
    03_Clustering
    Hierarchical Clustering Bit Vector Distances Molecule Descriptors
    +4
    This exercise shows how to perform hierarchical clustering using molecule fingerprints and create an interactive view to pick int…
    knime > Life Sciences > Events > 2021_09_13_Vienna_Summer_School > Advanced > solutions > 01_Clustering_Fingerprint_Similarity
    0
    knime
  10. Go to item
    Workflow
    01_Chemistry_basics
    Chemistry Interactive View Life Sciences
    +1
    This workflow demonstrates basic cheminformatics functionality within KNIME Analytics Platform: Reading and writing various chemi…
    knime > Life Sciences > Events > 2022_04_20_AIDD_Workshop > exercise > Chemistry_Exercise
    0
    knime
  11. Go to item
    Workflow
    04_SimilaritySearch
    Chemistry Shared Components Life Sciences
    +2
    In this exercise we expand our results by finding building blocks similar to those we selected in the previous exercise (03_Clust…
    knime > Life Sciences > Events > 2022_05_08_GCC > solution > Similarity_Search
    0
    knime
  12. Go to item
    Workflow
    03_Fetch_SMILES
    PubChem AWS Chemistry
    +4
    This is the third workflow in the PubChem Big Data story. First, we obtain the SMILES of the necessary CIDs using PubChem REST se…
    knime > Life Sciences > Cheminformatics > ChemistryFPs_vs_BiologyFPs > DataPrep > 03_Fetch_SMILES
    0
    knime
  13. Go to item
    Workflow
    04_Generate_Features
    Apache Spark KNIME Workflow Executor for Apache Spark KWEfAS
    +4
    This is the forth workflow in the PubChem Big Data story.
    knime > Life Sciences > Cheminformatics > ChemistryFPs_vs_BiologyFPs > DataPrep > 04_Generate_Features
    0
    knime
  14. Go to item
    Workflow
    03_Clustering
    Chemistry Hierarchical Clustering Bit Vector Distances
    +4
    This exercise shows how to perform hierarchical clustering using molecule fingerprints and create an interactive view to pick int…
    catherineoleary > Public > L4-CH Introduction to Working with Chemical Data > exercises > 03_Clustering
    0
    catherineoleary
  15. Go to item
    Workflow
    03a_Clustering_and_MCS Bonus material
    Hierarchical Clustering Bit Vector Distances Molecule Descriptors
    +4
    This exercise shows how to perform hierarchical clustering using molecule fingerprints and create an interactive view to pick int…
    catherineoleary > Public > L4-CH Introduction to Working with Chemical Data > solutions > 03a_Clustering and MCS
    0
    catherineoleary
  16. Go to item
    Workflow
    01_Chemistry_basics
    Chemistry Interactive View Life Sciences
    +1
    This workflow demonstrates basic cheminformatics functionality within KNIME Analytics platform: Reading and writing various chemi…
    catherineoleary > Public > L4-CH Introduction to Working with Chemical Data > solutions > 01_Chemistry_basics
    0
    catherineoleary
  17. Go to item
    Workflow
    01_Chemistry_basics
    Chemistry Interactive View Life Sciences
    +1
    This workflow demonstrates basic cheminformatics functionality within KNIME Analytics platform: Reading and writing various chemi…
    knime > Life Sciences > Events > 2022_04_20_AIDD_Workshop > solution > Chemistry_Manipulation_and_Visualization
    0
    knime
  18. Go to item
    Workflow
    04_SimilaritySearch
    Chemistry Shared Components Life Sciences
    +2
    In this exercise we expand our results by finding building blocks similar to those we selected in the previous exercise (03_Clust…
    catherineoleary > Public > L4-CH Introduction to Working with Chemical Data > solutions > 04_SimilaritySearch
    0
    catherineoleary
  19. Go to item
    Workflow
    pKa-Profile
    Chemistry
    R based node that generates a pH profile from pKa and whether compound is an acid or a base
    raelldata > Public > pKa-Profile
    0
    raelldata
  20. Go to item
    Workflow
    01_Fetch_BioAssays
    PubChem Chemistry AWS
    +7
    This is the first workflow in the PubChem Big Data story. In the top part of the workflow we download the assay data from the Pub…
    knime > Life Sciences > Cheminformatics > ChemistryFPs_vs_BiologyFPs > DataPrep > 01_Fetch_BioAssays
    0
    knime

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