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Tag: cheminformatics

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 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).

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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 #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 #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 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 Example PubChem, ChEBI and ChemSpider workflows


Created: 2010-07-23 11:13:09 | Last updated: 2010-07-23 11:21:05

This pack contains example pipelines showing how the PubChem, ChEBI and ChemSpider web services can be called from Taverna workflows. Descriptions of the operations found in the PubChem, ChEBI and ChemSpider web services are available at http://www.taverna.org.uk/introduction/related-projects/chemtaverna/chemistry-web-services. 

40 items in this pack

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Pack Mapping Metabolites for Metabolic Network Reconstruc...


Created: 2010-06-03 11:43:43 | Last updated: 2010-06-03 11:47:16

The process of metabolic network reconstructions typically begins with the task of collating existing information. For metabolites this poses a relatively straight forward set of cheminformatics problems. These problems include finding identical structures across sources, which is trivial, but also structures that differ due to idiosyncrasies of the sources or annotators. This includes charge differences, varying stereochemistry, tautomers, and so forth. Workflows in this pack allow sets of ...

6 items in this pack

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