Group: Cheminformatics

Overview

Workflows in the area of cheminformatics, for example, using ChemSpider or PubChem webservices, or using cheminformatics plugins like CDK-Taverna.

Created at: Thursday 04 December 2008 21:18:56 (UTC)

Unique name: cheminformatics

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  1. Avatar
    sauberns shared Indigo-pains-recursive
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    *** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries *** The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recurs …
    Tuesday 13 August 2013 08:06:44 (UTC)
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    Egon Willighagen shared Find isotopes with a certain exact match
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    This script lists all isotopes matching a certain exact mass (given a certain error) and outputs the symbol, atomic number, and exact match of the search hits.
    Tuesday 30 July 2013 20:53:34 (UTC)
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    sauberns shared Chemical structure extractor - img2structure
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    Extracts images of chemical structures from PDFs and converts them to usable structure data using the OSRA binaries. An in-progress (incomplete) workflow. This workflow makes use of the External Tool node to access the OSRA structure recognition binaries. So you must have a functioning installation o …
    Tuesday 14 May 2013 23:54:22 (UTC)
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    Paul Dobson shared CDK Example
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    This workflow reads a library from an SD file (change the default value of Read_MDL_SD_File) and identifies those structures that conform to Lipinski's Rule of Five. It then performs a substructure query, represented as SMILES (change the default value on Parse_SMILES), on the structures that pass Li …
    Wednesday 08 May 2013 14:51:56 (UTC)
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    sauberns shared Chemical term extractor - text2structure
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    This workflow demonstrates how to extract biological and chemical terms (text!) from a PDF file using the KNIME text processing nodes and attempts to convert the chemistry terms to structures. Requirements: KNIME 2.7.4 KNIME Labs nodes - Text Processing Community Nodes - RDKit (to view structures) Se …
    Tuesday 23 April 2013 11:23:29 (UTC)
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    Giribio, and Mcasfrox joined the Cheminformatics group
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    sauberns shared RDKit-bioisosteres
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    Implementation of a simple bioisostere replacement workflow using the RDKit (2.0.0) nodes in KNIME (2.5.1). Includes short list of classical bioisostere replacements (not exhaustive), selectable by the functional group to be transformed. We added this control to the workflow as our own internal list …
    Wednesday 18 January 2012 03:54:55 (UTC)
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    sauberns shared RDKit-pains-parallel
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    If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains, and Indigo-pains. *** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries *** *** This version contains Parallel processing nodes to take advantage of mutil-co …
    Friday 16 December 2011 04:07:16 (UTC)
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    Xyzmjf joined the Cheminformatics group
    Tuesday 13 December 2011 19:54:29 (UTC)
  10. Avatar
    sauberns shared RDKit-pains
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    If you like this workflow, please reference our paper doi:10.1002/minf.201100076, and check the related workflows RDKit-pains-parallel, and Indigo-pains. *** Update 20151119 - using KNIME 3 and RDKit version of PAINS queries *** Implementation of the PAINS filters[1] using the RDKit (3.0.0.2015111313 …
    Saturday 23 July 2011 02:28:50 (UTC)
  11. Avatar
    sauberns shared Indigo-pains
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    If you like this workflow, please reference our paper doi:10.1002/minf.201100076 , and check the related workflows Indigo-pains-recursive, and RDKit-pains. *** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries *** Implementation of the PAINS filters[1] using the Indigo (1 …
    Saturday 23 July 2011 02:28:01 (UTC)

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