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03 CCDC CSD Similarity Search

CCDC CSD Similarity Search

CCDC CSD Similarity Search

This example workflow illustrates the use of the CSD Similarity Search component. Queries may come from various sources and can be in MOL or MOL2 format. The similarity of the hit to the query is returned. This is calculated using the Tanimoto coefficient on 2D, path-based fingerprints.

CCDC CSD Similarity SearchThis example workflow illustrates the use of the CCDC CSD Similarity Search component. Queries may come from various sources and can be in MOL or MOL2 format. The similarity ofthe hit to the query is returned. This is calculated using the Tanimoto coefficient on 2D, path-based fingerprints.The notes on visualisation of hits and on search filters in the CCDC CSD Text-Numeric Searches example workflow apply to other search types, so they are not discussed again here.Example files to be used in these workflows are included in this archive: http://downloads.ccdc.cam.ac.uk/KNIME/Example_Workflows.zipDownload and extract the archive, then replace /path/to in any configuration file paths with the full path to the folder into which you extracted the archive. Here we use Lapatinib as a similarity-search query. Note that the Marvin Sketch node hasbeen configured to output MOL2 formatinstead of MOL format. The ' Load MOL files' utility is used to load multiple querystructures from a folder of MOL-format files. Double-clickthe component to configure it to point to the correct folderon your system.These structres were drawn in in Marvin Sketch andexported as MOL-format molfiles. Inspection will show thatthe hit-list is the same as in the SMILES example above. This example shows that suitable MOL-format queriesmay also be generated from SMILES input. Here weuse RDKit Nodes to perform the conversion (double-click the MetaNode to see the details). The data table may be exported to an Excel file.As multi-line strings are problematic in somecontexts, the MOL2 column and diagram areremoved before export. Note that the similaritythreshold has been set to 0.5 insead of the default of 0.7. Remove molfileQueries as SMILESView hitsDouble-click to accessthe individual filters.Write table CCDC CSDSimilarity Search MarvinSketch Column Filter Table Creator SMILES to MOL Table View CSD Search Filters Excel Writer (XLS) CCDC Run Mercury CCDC Load MOL files CCDC CSDSimilarity Search CCDC CSDSimilarity Search CCDC CSD Similarity SearchThis example workflow illustrates the use of the CCDC CSD Similarity Search component. Queries may come from various sources and can be in MOL or MOL2 format. The similarity ofthe hit to the query is returned. This is calculated using the Tanimoto coefficient on 2D, path-based fingerprints.The notes on visualisation of hits and on search filters in the CCDC CSD Text-Numeric Searches example workflow apply to other search types, so they are not discussed again here.Example files to be used in these workflows are included in this archive: http://downloads.ccdc.cam.ac.uk/KNIME/Example_Workflows.zipDownload and extract the archive, then replace /path/to in any configuration file paths with the full path to the folder into which you extracted the archive. Here we use Lapatinib as a similarity-search query. Note that the Marvin Sketch node hasbeen configured to output MOL2 formatinstead of MOL format. The ' Load MOL files' utility is used to load multiple querystructures from a folder of MOL-format files. Double-clickthe component to configure it to point to the correct folderon your system.These structres were drawn in in Marvin Sketch andexported as MOL-format molfiles. Inspection will show thatthe hit-list is the same as in the SMILES example above. This example shows that suitable MOL-format queriesmay also be generated from SMILES input. Here weuse RDKit Nodes to perform the conversion (double-click the MetaNode to see the details). The data table may be exported to an Excel file.As multi-line strings are problematic in somecontexts, the MOL2 column and diagram areremoved before export. Note that the similaritythreshold has been set to 0.5 insead of the default of 0.7. Remove molfileQueries as SMILESView hitsDouble-click to accessthe individual filters.Write table CCDC CSDSimilarity Search MarvinSketch Column Filter Table Creator SMILES to MOL Table View CSD Search Filters Excel Writer (XLS) CCDC Run Mercury CCDC Load MOL files CCDC CSDSimilarity Search CCDC CSDSimilarity Search

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: flatk
Created at: 2020-07-08
On NodePit since: 2020-09-10
Last update: 2024-11-17
Created with KNIME version: v4.1.3

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