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Isomer-augmentation-Data

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

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-isomer-augmentation

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

File type: application/x-zip-compressed

Comments: 0 | Viewed: 46 times | Downloaded: 26 times

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Alkane-Enumeration-Data

Created: 2017-06-30 16:57:41 | Last updated: 2017-10-12 13:45:28

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-isomer-transformation

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

File type: application/x-zip-compressed

Comments: 0 | Viewed: 44 times | Downloaded: 26 times

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Monomers-Data

Created: 2017-06-30 17:01:24 | Last updated: 2017-10-12 13:47:22

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-isomer-transformation

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

File type: application/x-zip-compressed

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Aminoglycosides-Data

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

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0-Mods-iQSAR

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

File type: application/x-zip-compressed

Comments: 0 | Viewed: 45 times | Downloaded: 25 times

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Cheminformatics

Unique name: cheminformatics
Created: Thursday 04 December 2008 21:18:56 (UTC)

11 shared items   |   0 announcements

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Bioclipse

Unique name: bioclipse
Created: Monday 13 September 2010 10:29:24 (UTC)

5 shared items   |   0 announcements

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Open PHACTS

Unique name: openphacts
Created: Friday 21 June 2013 13:19:22 (UTC)

26 shared items   |   0 announcements

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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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Mapping Metabolites for Metabolic Network Reconstruc...

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

6 items in this pack

Comments: 0 | Viewed: 86 times | Downloaded: 41 times

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Example PubChem, ChEBI and ChemSpider workflows

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

40 items in this pack

Comments: 0 | Viewed: 109 times | Downloaded: 33 times

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

Created: 2017-06-29 17:26:00 | Last updated: 2017-12-19 10:19:21

4 items in this pack

Comments: 0 | Viewed: 64 times | Downloaded: 28 times

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

Created: 2017-06-30 16:29:21 | Last updated: 2017-12-19 10:20:58

2 items in this pack

Comments: 0 | Viewed: 76 times | Downloaded: 21 times

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

Created: 2017-06-30 16:31:31 | Last updated: 2017-12-19 10:21:41

5 items in this pack

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

Created: 2017-06-30 16:33:44 | Last updated: 2017-12-19 10:22:03

3 items in this pack

Comments: 0 | Viewed: 52 times | Downloaded: 22 times

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Pack #4 - Metabolome completion and metabolomics

Created: 2017-06-30 16:36:44 | Last updated: 2017-12-19 10:22:42

2 items in this pack

Comments: 0 | Viewed: 55 times | Downloaded: 18 times

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Isosteric transform library

Created: 2020-04-27 13:23:39 | Last updated: 2020-04-27 13:29:56

1 item in this pack

Comments: 0 | Viewed: 105 times | Downloaded: 6 times

Create Ugi Library 001 (1)

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Created: 2008-12-04

Credits: Jean-Claude Bradley

Download from ChemSpider using Accurate Mass (2)

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No description

Created: 2007-11-26 | Last updated: 2008-02-05

Credits: Egon Willighagen

/me is having Bioclipse/XMPP/RDF fun.js (1)

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Created: 2009-08-21

Credits: Egon Willighagen

Visualize Molecules from DBPedia as Molecu... (3)

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Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

Created: 2010-03-14

Credits: Egon Willighagen

Open PDB entries in Jmol for hits found fo... (3)

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Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Created: 2010-03-14 | Last updated: 2010-06-23

Credits: Egon Willighagen

Download CAS numbers and save as SD file (1)

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Download molecules from a REST services using the CAS registry number, create 3D coordinates and save the results as a MDL SD file.

Created: 2009-10-15

Credits: Egon Willighagen

Determine the Maximum Common SubStructure ... (1)

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Created: 2009-10-23

Credits: Egon Willighagen

Kabsch Alignment of Small Molecules (1)

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Created: 2009-10-30

Credits: Egon Willighagen

Convert a SMILES string into a connection ... (1)

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Created: 2009-12-16

Credits:

Download all data sets from a OpenTox API ... (3)

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 Uses the OpenTox API (REST+RDF) to query all data sets, downloads them as MDL SD file, and opens the results in the Bioclipse molecules table.

Created: 2010-04-01 | Last updated: 2010-11-13

Credits:

Calculate molecular mass for entries in a ... (1)

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Created: 2010-03-08

Credits:

Download QSAR data sets using the OpenTox ... (1)

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Created: 2010-03-22

Credits: Egon Willighagen

C1 Combined Workflow (1)

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Created: 2010-06-03 | Last updated: 2010-06-03

Credits: Paul Dobson

M1 Exact Matching (1)

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Created: 2010-06-03

Credits: Paul Dobson

M2 Similarity Matching (1)

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Created: 2010-06-03

Credits: Paul Dobson

M3 Non-stereo Matching (1)

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Created: 2010-06-03

Credits: Paul Dobson

M4 Tautomer Matching (1)

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Created: 2010-06-03

Credits: Paul Dobson

M5 Charge Matching (1)

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Created: 2010-06-03

Credits: Paul Dobson

Generate inChi (1)

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Generates an inChi string for a given chemical represented by its SMILES string, SDF or MOL file using the inchi web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Generate inChi information (1)

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Uses the GenerateInchiInfo web service operation from ChemSpider to generate information relating to the InChi string for a given chemical compound

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Generate InChi key (1)

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Generates an inchi key for a given compound using the inchi web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to ChemSpider identifier (1)

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Returns Converts an InChIKey to a ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to Inchi string (1)

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Converts an InChI key to an InChI string using the ChemSpider Inchi web service.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChi key to MOL file (1)

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Returns a MOL file for a given InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIToCSID (1)

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Convert InChI to ChemSpider ID

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIStringToInChiKey (1)

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Converts an InChI string to an InChi key

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InChIStringToMolFile (1)

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Converts an InChI string into a MOL file using the Inchi ChemSpider web service

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

InchiStringToSmiles (1)

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Converts an inchi string into SMILES format

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

isValidInChiKey (1)

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Checks that specified argument is valid InChIKey. Works for v1.02b InChIKey only.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

MolToInchiString (1)

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Converts a MOL file to InChI. Result is v1.02s InChI.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

MolToInchiKey (1)

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Converts a MOL file to an InChIKey. Result is v1.02s InChIKey.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

SmilesToInchi (1)

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Convert SMILES to InChI. Result is v1.02s InChI.

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Convert chemical identifier (1)

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Converts a chemical compound identifier from one format to another using the open babel web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: Peter Li

Get list of chemspider databases (1)

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Returns a list of databases catalogedReturns a list of databases cataloged by ChemSpider

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get extended compound information (1)

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Returns information from chemspider for a given chemical represented by its chemspider identifier

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get extended compound information for a li... (1)

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 Returns information for a given list of chemspider compound identifiers.

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get ChemSpider record in MOL format (1)

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Returns ChemSpider record in MOL format or empty string in case of failure.

Created: 2010-07-12 | Last updated: 2010-07-12

Credits: Peter Li

Get spectra information (1)

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Returns information about the spectra stored in ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound spectra information (1)

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Returns information about spectra stored in ChemSpider for a given compound represented by its chemspider identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get spectrum information (1)

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Returns information about a spectrum identified by its chemspider spectrum identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Asynchronous chemspider simple search (1)

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Performs an asynchronous simple search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound information (1)

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Returns information about a given compound represented by its chemspider id

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get compound thumbnail (1)

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Returns a small image of the 2D structure of given chemical compound represented by its chemspider identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get structure synonyms (1)

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Returns synonyms for a given compound represented by a MOL fileReturns synonyms for a given compound

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

chemspider identifier to MOL format (1)

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Returns the MOL file for a given compound represented by its chemspider identifier

Created: 2010-07-13

Credits: Peter Li

getLiteEntity (1)

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Retrieves a list of "lite" entities containing only the ChEBI ASCII name and ChEBI identifier. The input parameters are a search string and a search category. If the search category is null then it will search under all fields. The search string accepts the wildcard character "*" and also unicode characters. You can get maximum results upto 5000 entries at a time.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Asynchronous chemspider search by formula (1)

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Performs an asynchronous search on ChemSpider by molecular formula

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get complete chebi entity (1)

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Returns informations for a given compound represented by its chebi identifier

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get complete entity by list (1)

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Returns information from the chebi database for a list of chebi identifiers

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get ontology parents (1)

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Get ontology children (1)

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Retrieves the ontology children of an entity including the relationship type, using the ChEBI identifier.

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Search structures in ChEBI database (1)

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 Does a substructure, similarity or identity search using a structure in the Chebi database

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

Simple search (1)

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Performs a lite search on ChemSpider

Created: 2010-07-13 | Last updated: 2010-07-13

Credits: Peter Li

file-similarity-entrez-url (2)

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Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

smiles-identity-idlist (1)

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Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

smiles-identity-idlist (2)

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Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

PubChem substructure search (2)

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Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

download (2)

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Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Created: 2010-07-16 | Last updated: 2010-07-16

Credits: Peter Li

Predict chemical solubility in solvents (2)

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Predicts solubility in molar units for a given chemical compound represented as a SMILES string in a given solvent. Uses a beanshell script to enable the user to select the solvent from a list.

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Peter Li

Predict Abraham descriptors (1)

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Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values. The workflow returns all the Abraham descriptors E, S, A, B and V in a HTML file.Predicts descriptor values using a model derived from a linear regression analysis of the Open Notebook Science solubility data and literature values

Created: 2010-08-05 | Last updated: 2010-08-05

Credits: Peter Li

Generate CombiUgi library (1)

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Generates a CombiUgi library using data from a Goolgle spreadsheet containing smiles strings of compounds to undergo virtual Ugi reactions

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Peter Li Romney

Visualize the boiling point data from the ... (1)

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 Downloads the RDF data from a HTML page, extracts the boiling point data, calculates atom counts from SMILES representations, and opens the data in a matrix editor, ready to be visualized in a scatter plot.

Created: 2010-08-10 | Last updated: 2010-08-10

Credits: Egon Willighagen

Calculate molecular descriptors with OpenT... (1)

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 Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules.

Created: 2010-10-30 | Last updated: 2010-10-30

Credits: Egon Willighagen

Run OpenTox models on local data. (1)

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 Runs a remote OpenTox model to predict properties for local data which is uploaded on the fly.

Created: 2010-11-13 | Last updated: 2010-11-13

Credits: Egon Willighagen

QSPR Model Discovery -- workflow structure... (2)

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replicates the structure of the QSPR model discovery workflow. Ref.: replicates the structure of the QSPR model discovery workflow. Ref.: http://www.openqsar.com/

Created: 2011-01-18 | Last updated: 2011-01-18

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: sauberns

Attributions: Indigo-pains

Extract chemical structures from a Beilste... (1)

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 Uses the Oscar4 text mining tool to extract chemical structures from a Beilstein Journal of Organic Chemistry paper and visualizes them in the molecules table. Jericho is used to extract text from the paper's HTML page.

Created: 2011-05-12 | Last updated: 2011-05-12

Credits: Egon Willighagen

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

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: sauberns

Attributions: RDKit-pains

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: sauberns

Attributions: RDKit-pains

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: sauberns

Attributions: RDKit-pains

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: sauberns

Attributions: Chemical structure extractor - img2structure

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: sauberns

Attributions: Chemical term extractor - text2structure

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: sauberns

Attributions: Indigo-pains RDKit-pains-parallel

Chemical2URIs (1)

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This workflow will map a chemical name or identifier to uniform resource identifiers (URIs). First the ChemSpider web service is used to map the chemical name to a ChemSpider identifier, then the ChemSpider identifier is mapped to URIs via the Open PHACTS platform.

Created: 2015-08-18

Credits: Kristina Hettne Eelke van der Horst BioSemantics

RetroPath2.0-Mods-isomer-augmentation (2)

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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.Licence: CC BY-NC-SAThis 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/.Koch M, D...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

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

RetroPath2.0-Mods-isomer-transformation (2)

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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.Licence: CC BY-NC-SAThis 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/licen...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

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

QSAR-model-Tg-prediction (2)

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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.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. T...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-iQSAR (2)

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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.Licence: CC BY-NC-SAThis 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/...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

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

QSAR-model-aminoglycosides (2)

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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.Licence: CC BY-NC-SAThis work is licensed under the Creative Commons Attribution-NonCo...

Created: 2017-06-30 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

RetroPath2.0-Mods-metabolomics (2)

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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: 2018-11-14

Credits: Thomas Duigou BioRetroSynth

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

RetroPath2.0-Mods-isomer-transformation-queue (2)

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The workflow allows one to enumerate isomers of chemical structure(s) using the isomer transformation algorithm. It is a modified version of "RetroPath2.0-Mods-isomer-transformation". It illustrates how to introduce a FIFO data structure for the source set and use it for iteratively firing rules on small chunks of structures. See [1] for details. How to useSee instructions embedded in the workflow.Usage specificationsThe workflow is compatible starting from version 3.4.1 of Kni...

Created: 2017-10-12 | Last updated: 2017-12-19

Credits: Thomas Duigou BioRetroSynth

Attributions: RetroPath2.0 - a retrosynthesis workflow with tutorial and example data RetroPath2.0-Mods-isomer-transformation

Genetic Algorithms for BIOISOSTERIC Struct... (1)

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Genetic algorithm workflow to generate novel structures by recombination and mutation and that uses an ML model as a fitness function. Both the fitness function and the fingerprints modified in the model should be the same. ML model cannot have any descriptors other than given fingerprint.Reverse molecular mapping/generation is not part of this workflow and can be done by creating a large Structure-FP database.

Created: 2018-11-06

Credits: Insilicoconsulting