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Items tagged with "chemoinformatics" (27)

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Blob Isomer-augmentation-Data

Created: 2017-06-30 16:49:46 | Last updated: 2017-06-30 17:12:54

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-isomer-augmentation

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-isomer-augmentation workflow:- Source and Rules input.- Pre-generated Results.

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Blob Alkane-Enumeration-Data

Created: 2017-06-30 16:57:41 | Last updated: 2017-06-30 17:12:09

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-isomer-transformation

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-isomer-transformation workflow for the alkane enumeration use case:- Source and Rules input.- Pre-generated Results.

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Blob Monomers-Data

Created: 2017-06-30 17:01:24 | Last updated: 2017-06-30 17:10:45

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-isomer-transformation

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-isomer-augmentation and QSAR-model-Tg-prediction workflows for the monomer enumeration use case:- Source and Rules input.- Pre-generated Results.- Training set for building the QSAR of the glass transition temperature.

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Blob Aminoglycosides-Data

Created: 2017-06-30 17:09:48 | Last updated: 2017-07-03 08:19:12

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0-Mods-iQSAR

License: Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License

Data to be used with the RetroPath2.0-Mods-iQSAR and QSAR-model-aminoglycosides workflows for the "search for molecules maximizing biological activities" use case:- Source and Rules input.- Pre-generated Results.- Training set for building the QSAR of the antibacterial activity.

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Packs (7)

Pack useful_for_sysmo


Created: 2008-12-17 12:31:48 | Last updated: 2009-06-10 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

21 items in this pack

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Pack Natural product likeness filter


Created: 2011-05-13 19:35:39 | Last updated: 2011-08-29 14:25:47

Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work...

3 items in this pack

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Pack KNIME workflows and associated data from Koch et. al...


Created: 2017-06-29 17:26:00 | Last updated: 2017-06-30 18:12:11

The pack provides the KNIME workflows and associated data from Koch et. al., Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 2017.Please browse the linked packs below.

4 items in this pack

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Pack Pack #1 - Isomer enumeration (canonical augmentation...


Created: 2017-06-30 16:29:21 | Last updated: 2017-06-30 17:58:54

This pack provides part of the supporting material for M. Koch et. al., Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 2017.The pack contains the (i) RetroPath2.0-Mods-isomer-augmentation worklfow as well as (ii) the associated data for the enumeration of isomers using the canonical augmentation algorithm (see the main text for details, section 2.1 "Isomer enumeration").

2 items in this pack

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Pack Pack #2 - Isomer enumeration (isomer transformation ...


Created: 2017-06-30 16:31:31 | Last updated: 2017-06-30 18:00:35

This pack provides part of the supporting material for M. Koch et. al., Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 2017.The pack contains (i) the RetroPath2.0-Mods-isomer-transformation worklfow, (ii) data for the enumeration of alkane isomers using the isomer transformation algorithm (see the main text for details, section 2.1 Isomer enumeration), (iii) data to be used for the enumeration of isomers of monomers as well as (iv) the...

4 items in this pack

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Pack Pack #3 - Search for molecules maximizing biological...


Created: 2017-06-30 16:33:44 | Last updated: 2017-06-30 18:01:34

This pack provides part of the supporting material for M. Koch et. al., Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 2017.The pack contains (i) the RetroPath2.0-Mods-iQSAR workflow for the search of molecules of interest, (ii) the QSAR-model-aminoglycosides workflow that build a QSAR model for predicting the antibacterial activity, and (iii) the associated data to be used with the two workflows (see the main text for details, section...

3 items in this pack

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Pack Pack #4 - Metabolome completion and metabolomics


Created: 2017-06-30 16:36:44 | Last updated: 2017-06-30 18:04:28

This pack provides part of the supporting material for M. Koch et. al., Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. bioRxiv, 2017.The pack contains (i) the RetroPath2.0-Mods-metabolomics workflow as well as (ii) all the associated data for the metabolome completion use case (see the main text for details, section 2.4 Metabolome completion and metabolomics).

2 items in this pack

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Workflows (16)
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Workflow RDKit-pains (4)

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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 (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the SMARTS form of the filters published by Greg Landrum as part of the RDKit library[2], whic...

Created: 2011-02-07 | Last updated: 2015-11-19

Credits: User sauberns

Attributions: Workflow Indigo-pains

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Workflow Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: User Kalai

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Workflow Scoring small molecules for metabolite lik... (2)

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: User Kalai

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Workflow Plotting distribution of natural product l... (1)

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: User Kalai

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Workflow Indigo-pains (2)

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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 (1.1.1300.201511201230) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. his workflow contains the SMARTS form of the filters published by Greg Landrum as part of th...

Created: 2011-06-07 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow RDKit-pains

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Workflow RDKit-pains-parallel (2)

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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-core processors ***Implementation of the PAINS filters[1] using the RDKit (3.0.0.201511131320) nodes in KNIME (3.0.1). Original PAINS filters were published in SLN format. This workflow contains the S...

Created: 2011-10-13 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow RDKit-pains

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Workflow RDKit-bioisosteres (1)

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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 of bioisostere replacements generated huge libraries for each structure fed into the workflow. The bioisostere replacement list is stored in a tab separated text file, so can be replaced...

Created: 2012-01-18 | Last updated: 2012-01-18

Credits: User sauberns

Attributions: Workflow RDKit-pains

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Workflow Chemical term extractor - text2structure (1)

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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 2.7.4KNIME Labs nodes - Text ProcessingCommunity Nodes - RDKit (to view structures)See http://tech.knime.org/communityStart by selecting the folder containing the PDF documents. Alternatively, you can use a folder with Word docs.

Created: 2013-04-22 | Last updated: 2013-04-22

Credits: User sauberns

Attributions: Workflow Chemical structure extractor - img2structure

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Workflow Chemical structure extractor - img2structure (1)

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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 of OSRA and it's dependencies. This may require advanced compiler knowledge on your platform, and may not be a trivial task.OSRA 1.4 is free for both the source & binary distribution. OSRA 2.0...

Created: 2013-05-14 | Last updated: 2013-05-14

Credits: User sauberns

Attributions: Workflow Chemical term extractor - text2structure

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Workflow Indigo-pains-recursive (2)

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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 recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list.Using the WEHI-10k reference set (embedded in ...

Created: 2013-08-13 | Last updated: 2015-12-01

Credits: User sauberns

Attributions: Workflow Indigo-pains Workflow RDKit-pains-parallel

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Workflow RetroPath2.0-Mods-isomer-augmentation (1)

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The workflow allows one to enumerate isomers using the isomer augmentation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/. [1] M. Koch, T. ...

Created: 2017-06-30 | Last updated: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

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Workflow RetroPath2.0-Mods-isomer-transformation (1)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/...

Created: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

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Workflow QSAR-model-Tg-prediction (1)

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The workflow (i) build a QSAR model for Tg prediction with LOO cross-validation and (ii) predict the Tg for enumerated isomers. See [1] for details. Tg values were compiled from Brown et al, JCIM, 2006. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy...

Created: 2017-06-30 | Last updated: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

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Workflow RetroPath2.0-Mods-iQSAR (1)

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The workflow allows one to search chemical structures in the chemical space optimizing biological activites. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/...

Created: 2017-06-30 | Last updated: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

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Workflow QSAR-model-aminoglycosides (1)

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The workflow build a QSAR model with LOO cross-validation for antibacterial activities of aminoglycosides structures using RDKit fingerprints and random forest. See [1] for details. Antibacterial activities were compiled from Setny et al, JCIM, 2009. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.3.2 of Knime Analytics Platform.LicenceThis work is licensed under the Creative Commons Attribution-NonCommercial-Shar...

Created: 2017-06-30 | Last updated: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

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Workflow RetroPath2.0-Mods-metabolomics (1)

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Set of workflows for the "Metabolome completion and metabolomics" use case:1) Produces a list of molecules using a user defined set of rules (RetroPath2.0 workflow).2) Takes as input the products generated by RetroPath2.0 and prepare the files to be read by OpenMS nodes.3) The last workflow finally searches for each produced compound the corresponding peak in some MS spectra.See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflo...

Created: 2017-06-30 | Last updated: 2017-06-30

Credits: User Thomas Duigou Network-member BioRetroSynth

Attributions: Workflow RetroPath2.0 - a retrosynthesis workflow with tutorial and example data

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