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InviteGroup: CDK-Taverna
The CDK-Taverna plug-in provides chemoinformatic functionality to Taverna. This group contains workflows using the CDK-Taverna plug-in.
Created at: Friday 29 August 2008 @ 10:08:28 (GMT)
Unique name: CDKTaverna
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Workflow
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Created: 29/08/08 @ 09:59:06 | Last updated: 29/08/08 @ 10:17:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow reads the molecules form the an MDL SD File and stores them into a database. The database used here is a Postgres SQL database which uses the PGChem::Tigress chemoinformtic extension.
To run this workflow you have to install the CDK-Taverna Plug-in for Taverna 1.7.1.0 from http://cdk-taverna.de/plugin
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Created: 29/08/08 @ 13:31:12 | Last updated: 29/08/08 @ 13:40:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow loads molecules from a database. Each molecule goes through the atom typing, gets its explecite hydrogens and the detection of the hueckel aromaticity. After that different qsar properties will be calculated. The output of this workflow will be a qsar vector as a csv file and a file which contains the time needed to calculate each qsar property.
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Created: 06/09/08 @ 11:08:43
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow loads molecules from a database. For each molecule the atom type gets perceived. The output of this workflow are a couple of text files. The frist text file contains all molecule id's which are loaded from the database. The second text file contains all molecules which had problems with the atom typing. This file contains the molecule id and the atom which caused the problem. The last output file, a pdf, contains all structures of the molecules which caused problems during the a...
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Created: 03/11/08 @ 14:28:31
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow loads molecules from a database in an iterative manner using the SQL commands LIMIT and OFFSET.
After the loading each molecule goes through an atom typing perception before the Hueckel Aromaticity Detector tries to detect the aromaticity. All id of the aromatic molecules will be written wo a text file.
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Created: 05/11/08 @ 10:30:38
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow load molecules into a database. The molecules originally are stored in a MDL SD file. As workflow input an origin is added to each molecule which gets stored into the database. The output of the workflow shows logs from the database insert process.
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Created: 05/11/08 @ 16:15:58
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow loads molecules from a database. The 2D structure of these molecules are shown within a table of a PDF document.
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Created: 05/11/08 @ 17:30:37
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow load molecules from the database and than checks whether the perception of the atom types works or not. After the extraction of the database identifier from all molecules which caused problems during this process will the identifier be written to a file.
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Workflow
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Created: 06/11/08 @ 12:02:18
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow takes as input a SMILES. This represents the substructure, for which the database gets searched. The output of this workflow is a PDF showing the 2D structures of the matched structure from the substructure search on the database.
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Created: 06/11/08 @ 16:11:54
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This worklfow load a TSV file from the ChEBI database. (normally structures.tsv) After the extraction of the molecules from the TSV file all non MDL mol files are removed before the valid molecules are inserted into a database.
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Created: 06/11/08 @ 16:59:02
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs a topological substructure search. The molecules to be searched are loaded from a MDL SD file. The substructure is loaded from a SMILES (workflow input). The matched molecules are converted to CML and for the molecules which do not contain the substructure the InChI is generated.
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Created: 06/11/08 @ 22:25:28
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow is used to analyse the result of the atom typing workflow. It creates a pdf document contains a diagram to visualise the outcome from the atom typing test to detect the for the cdk unknown atom types.
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Created: 07/11/08 @ 14:18:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow calculates the molecular weight of molecules stored in a postgres sql database with the Pgchem::tigress chemoinformatics cardridge. The cardridge perform the molecular weight calculation. The get a moleculear weight distribution worker creates a chart of the available data.
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Created: 15/11/08 @ 15:12:05
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow loads iteratively molecules from a database. For each molecule the atom typse are perceived before the hydrogens are added and the aromaticity is detected. Than the QSAR worker calculates the selected descriptors. The result of this calculation is stored in database table.
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Created: 17/11/08 @ 13:48:19
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow loads a vector from a database and performs an ART2A classification. The ART2A classificator contains various options which are changeable within the stored workflow configuration file. There is no UI for these content available.
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Created: 17/11/08 @ 14:21:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow load an ART2A classifcation results and creates a diagram showing the origin allocation within the different cluster or classes. This is usable for performing a chemical diversity analysis. The result is stored within an PDF which contains a diagram and a table of the classification result.
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Created: 21/11/08 @ 15:25:01
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. This SD-Files contains molecules for the enumeration. The products of the enumerated reaction are stored as Mol Files and a PDF will be created which contains the product molecules.
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Created: 22/11/08 @ 16:55:34
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. This SD-Files contains molecules for the enumeration. The products of the enumerated reaction are stored as Mol Files and a PDF will be created which contains the product molecules.
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Created: 26/02/09 @ 16:31:21
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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 Lipinski, and creates PNG images of those structures that contain the substructure.
The image results will be found in your Taverna Data folder.
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File
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Created: 27/02/08 @ 16:21:30 | Last updated: 12/01/12 @ 21:12:15
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
A Pipeline Pilot protocol to search ChemSpider by structure (smiles string) to illustrate use of the ChemSpider wsdl
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Created: 13/05/11 @ 17:14:06 | Last updated: 13/05/11 @ 19:47:24
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
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