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useful_for_sysmo

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

21 items in this pack

Comments: 0 | Viewed: 254 times | Downloaded: 48 times

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Natural product likeness filter

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

3 items in this pack

Comments: 0 | Viewed: 198 times | Downloaded: 90 times

Insert Molecules into Database (1)

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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

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

QSAR workflow to measure the time used for... (1)

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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.

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

Atom typing of molecules from database (1)

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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...

Created: 2008-09-06

Credits: Thomasku

Iterative loading of molecules from databa... (1)

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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.

Created: 2008-11-03

Credits: Thomasku

InsertMoleculesIntoDatabase (1)

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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.

Created: 2008-11-05

Credits: Thomasku

Load Molecules from a database and create ... (1)

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This workflow loads molecules from a database. The 2D structure of these molecules are shown within a table of a PDF document.

Created: 2008-11-05

Credits: Thomasku

Extraction of atom typing problems after l... (1)

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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.

Created: 2008-11-05

Credits: Thomasku

Substructure Search On Database (1)

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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.

Created: 2008-11-06

Credits: Thomasku

Extract ChEBI molecules from TSV file and ... (1)

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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.

Created: 2008-11-06

Credits: Thomasku

Topological Substructure Search Workflow (1)

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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.

Created: 2008-11-06

Credits: Thomasku

Analyse the Atom Typing Result (1)

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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.

Created: 2008-11-06

Credits: Thomasku

Molecular Weight Distribution (1)

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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.

Created: 2008-11-07

Credits: Thomasku

Calculation of molecular descriptors for m... (1)

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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.

Created: 2008-11-15

Credits: Thomasku

ART2A Classification Workflow (1)

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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.

Created: 2008-11-17

Credits: Thomasku

Get ART2A classification result showing th... (1)

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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.

Created: 2008-11-17

Credits: Thomasku

Reaction Enumeration Workflow (1)

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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.

Created: 2008-11-21

Credits: Thomasku

Reaction Enumeration Workflow (1)

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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.

Created: 2008-11-22

Credits: Thomasku

Attributions: Reaction Enumeration 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: Kalai

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: Kalai

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: Kalai