Tag Results

Items tagged with "cheminformatics" (97)

Note: some items may not be visible to you, due to viewing permissions.


Files (4)
Uploader

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.

File type: application/x-zip-compressed

Comments: 0 | Viewed: 17 times | Downloaded: 7 times

Tags:

Uploader

Blob Alkane-Enumeration-Data

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

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.

File type: application/x-zip-compressed

Comments: 0 | Viewed: 17 times | Downloaded: 8 times

Tags:

Uploader

Blob Monomers-Data

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

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.

File type: application/x-zip-compressed

Comments: 0 | Viewed: 18 times | Downloaded: 5 times

Tags:

Uploader

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.

File type: application/x-zip-compressed

Comments: 0 | Viewed: 17 times | Downloaded: 8 times

Tags:

Groups (3)

Network-member Cheminformatics

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

Workflows in the area of cheminformatics, for example, using ChemSpider or PubChem webservices, or using cheminformatics plugins like CDK-Taverna.

11 shared items   |   0 announcements

Tags:

Network-member Bioclipse

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

 Group around Bioclipse Scripting Language workflows.

5 shared items   |   0 announcements

Tags:

Owner

Network-member Open PHACTS

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

To reduce the barriers to drug discovery in industry, academia and for small businesses, the Open PHACTS consortium is building the Open PHACTS Discovery Platform. This will be freely available, integrating pharmacological data from a variety of information resources and providing tools and services to question this integrated data to support pharmacological research. 

26 shared items   |   0 announcements

Tags:

Packs (8)

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

Comments: 0 | Viewed: 227 times | Downloaded: 36 times

Tags:

Creator

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

Comments: 0 | Viewed: 69 times | Downloaded: 37 times

Tags:

Creator

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

Comments: 0 | Viewed: 98 times | Downloaded: 30 times

Tags:

Creator

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


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

The pack provides the KNIME workflows and associated data from:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9Please browse the linked packs below.

4 items in this pack

Comments: 0 | Viewed: 24 times | Downloaded: 7 times

Tags:

Creator

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


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

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The 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 items in this pack

Comments: 0 | Viewed: 41 times | Downloaded: 4 times

Tags:

Creator

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


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

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The 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 enumer...

5 items in this pack

Comments: 0 | Viewed: 24 times | Downloaded: 2 times

Tags:

Creator

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


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

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The 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) t...

3 items in this pack

Comments: 0 | Viewed: 21 times | Downloaded: 6 times

Tags:

Creator

Pack Pack #4 - Metabolome completion and metabolomics


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

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The 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 metabolo...

2 items in this pack

Comments: 0 | Viewed: 23 times | Downloaded: 4 times

Tags:

Workflows (82)

Workflow Create Ugi Library 001 (1)

Creates a virtual library of SMILES codes for all possible combinations of Ugi products based on lists of SMILES of starting materials in a Google Spreadsheet.  Uses Rajarshi Guha's web service. Can someone create a Taverna workflow that does this?

Created: 2008-12-04

Credits: User Jean-Claude Bradley

Workflow Download from ChemSpider using Accurate Mass (2)

Thumb
No description

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

Credits: User Egon Willighagen

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

Bioclipse script that combines RDF (DBPedia), XMPP cloud services, and local CDK functionality to gain some information on Farnesol in Bioclipse.

Created: 2009-08-21

Credits: User Egon Willighagen

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

Thumb
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: User Egon Willighagen

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

Thumb
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: User Egon Willighagen

Workflow Download CAS numbers and save as SD file (1)

Thumb
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: User Egon Willighagen

Workflow Determine the Maximum Common SubStructure ... (1)

BSL script to determine the maximum common substructure (MCSS) of a list of molecules and opens this in a JChemPaint editor.

Created: 2009-10-23

Credits: User Egon Willighagen

Workflow Kabsch Alignment of Small Molecules (1)

Aligns molecules using the Kabsch alignment and visualizes the results in the Jmol viewer.

Created: 2009-10-30

Credits: User Egon Willighagen

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

 Bioclipse script that converts a SMILES string into a LaTeX table of the connection table of the molecule.

Created: 2009-12-16

Credits: User

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

Thumb
 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: User

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

 Simple script to demonstrate how to iterate over entries in a MDL SD file and calculate some molecular property.

Created: 2010-03-08

Credits: User

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

 Bioclipse script that uses the OpenTox API 1.1 to download all QSAR data sets from a given service.

Created: 2010-03-22

Credits: User Egon Willighagen

Workflow C1 Combined Workflow (1)

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. This workflow implements matching algorithms M1-M5 in one workflow, yielding a sparse matrix of matches annotated by match types.

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

Credits: User Paul Dobson

Workflow M1 Exact Matching (1)

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. This workflow implements matching algorithm M1 which matches fully specified molecules on the basis of their canonical representations.

Created: 2010-06-03

Credits: User Paul Dobson

Workflow M2 Similarity Matching (1)

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. This workflow implements matching algorithm M2 which reads molecules from two sources and produces clusters of highly similar molecules.

Created: 2010-06-03

Credits: User Paul Dobson

Workflow M3 Non-stereo Matching (1)

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. This workflow implements matching algorithm M3 which strips stereochemical information from molecules, performs exact matching, and restores stereochemistry.

Created: 2010-06-03

Credits: User Paul Dobson

Workflow M4 Tautomer Matching (1)

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. This workflow implements matching algorithm M4 which generates canonical tautomers prior to matching, matches, then restores original structures.

Created: 2010-06-03

Credits: User Paul Dobson

Workflow M5 Charge Matching (1)

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. This workflow implements matching algorithm M5 which ionises molecules at pH 7 prior to matching, restores original structures.

Created: 2010-06-03

Credits: User Paul Dobson

Uploader

Workflow Generate inChi (1)

Thumb
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: User Peter Li

Uploader

Workflow Generate inChi information (1)

Thumb
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: User Peter Li

Uploader

Workflow Generate InChi key (1)

Thumb
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: User Peter Li

Uploader

Workflow InChi key to ChemSpider identifier (1)

Thumb
Returns Converts an InChIKey to a ChemSpider ID

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

Credits: User Peter Li

Uploader

Workflow InChi key to Inchi string (1)

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

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

Credits: User Peter Li

Uploader

Workflow InChi key to MOL file (1)

Thumb
Returns a MOL file for a given InChi key

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

Credits: User Peter Li

Uploader

Workflow InChIToCSID (1)

Thumb
Convert InChI to ChemSpider ID

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

Credits: User Peter Li

Uploader

Workflow InChIStringToInChiKey (1)

Thumb
Converts an InChI string to an InChi key

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

Credits: User Peter Li

Uploader

Workflow InChIStringToMolFile (1)

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

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

Credits: User Peter Li

Uploader

Workflow InchiStringToSmiles (1)

Thumb
Converts an inchi string into SMILES format

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

Credits: User Peter Li

Uploader

Workflow isValidInChiKey (1)

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

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

Credits: User Peter Li

Uploader

Workflow MolToInchiString (1)

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

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

Credits: User Peter Li

Uploader

Workflow MolToInchiKey (1)

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

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

Credits: User Peter Li

Uploader

Workflow SmilesToInchi (1)

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

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

Credits: User Peter Li

Uploader

Workflow Convert chemical identifier (1)

Thumb
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: User Peter Li

Uploader

Workflow Get list of chemspider databases (1)

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

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

Credits: User Peter Li

Uploader

Workflow Get extended compound information (1)

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

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

Credits: User Peter Li

Uploader

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

Thumb
 Returns information for a given list of chemspider compound identifiers.

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

Credits: User Peter Li

Uploader

Workflow Get ChemSpider record in MOL format (1)

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

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

Credits: User Peter Li

Uploader

Workflow Get spectra information (1)

Thumb
Returns information about the spectra stored in ChemSpider

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

Credits: User Peter Li

Uploader

Workflow Get compound spectra information (1)

Thumb
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: User Peter Li

Uploader

Workflow Get spectrum information (1)

Thumb
Returns information about a spectrum identified by its chemspider spectrum identifier

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

Credits: User Peter Li

Uploader

Workflow Asynchronous chemspider simple search (1)

Thumb
Performs an asynchronous simple search on ChemSpider

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

Credits: User Peter Li

Uploader

Workflow Get compound information (1)

Thumb
Returns information about a given compound represented by its chemspider id

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

Credits: User Peter Li

Uploader

Workflow Get compound thumbnail (1)

Thumb
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: User Peter Li

Uploader

Workflow Get structure synonyms (1)

Thumb
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: User Peter Li

Uploader

Workflow chemspider identifier to MOL format (1)

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

Created: 2010-07-13

Credits: User Peter Li

Uploader

Workflow getLiteEntity (1)

Thumb
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: User Peter Li

Uploader

Workflow Asynchronous chemspider search by formula (1)

Thumb
Performs an asynchronous search on ChemSpider by molecular formula

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

Credits: User Peter Li

Uploader

Workflow Get complete chebi entity (1)

Thumb
Returns informations for a given compound represented by its chebi identifier

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

Credits: User Peter Li

Uploader

Workflow Get complete entity by list (1)

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

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

Credits: User Peter Li

Uploader

Workflow Get ontology parents (1)

Thumb
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: User Peter Li

Uploader

Workflow Get ontology children (1)

Thumb
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: User Peter Li

Uploader

Workflow Search structures in ChEBI database (1)

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

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

Credits: User Peter Li

Uploader

Workflow Simple search (1)

Thumb
Performs a lite search on ChemSpider

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

Credits: User Peter Li

Uploader

Workflow file-similarity-entrez-url (2)

Thumb
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: User Peter Li

Uploader

Workflow smiles-identity-idlist (1)

Thumb
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: User Peter Li

Uploader

Workflow smiles-identity-idlist (2)

Thumb
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

Uploader

Workflow PubChem substructure search (2)

Thumb
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

Uploader

Workflow download (2)

Thumb
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: User Peter Li

Uploader

Workflow Predict chemical solubility in solvents (2)

Thumb
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: User Peter Li

Uploader

Workflow Predict Abraham descriptors (1)

Thumb
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: User Peter Li

Uploader

Workflow Generate CombiUgi library (1)

Thumb
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: User Peter Li User Romney

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

Thumb
 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: User Egon Willighagen

Workflow Calculate molecular descriptors with OpenT... (1)

Thumb
 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: User Egon Willighagen

Workflow Run OpenTox models on local data. (1)

Thumb
 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: User Egon Willighagen

Uploader

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

Thumb
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

Uploader

Workflow RDKit-pains (4)

Thumb
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

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

Thumb
 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: User Egon Willighagen

Uploader

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

Thumb
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: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

Uploader

Workflow Indigo-pains (2)

Thumb
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

Uploader

Workflow RDKit-pains-parallel (2)

Thumb
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

Uploader

Workflow RDKit-bioisosteres (1)

Thumb
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

Uploader

Workflow Chemical term extractor - text2structure (1)

Thumb
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

Uploader

Workflow Chemical structure extractor - img2structure (1)

Thumb
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

Uploader

Workflow Indigo-pains-recursive (2)

Thumb
*** 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

Workflow Chemical2URIs (1)

Thumb
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: User Kristina Hettne User Eelke van der Horst Network-member BioSemantics

Uploader

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

Thumb
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: User Thomas Duigou Network-member BioRetroSynth

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

Uploader

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

Thumb
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: User Thomas Duigou Network-member BioRetroSynth

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

Uploader

Workflow QSAR-model-Tg-prediction (2)

Thumb
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: User Thomas Duigou Network-member BioRetroSynth

Uploader

Workflow RetroPath2.0-Mods-iQSAR (2)

Thumb
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: User Thomas Duigou Network-member BioRetroSynth

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

Uploader

Workflow QSAR-model-aminoglycosides (2)

Thumb
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: User Thomas Duigou Network-member BioRetroSynth

Uploader

Workflow RetroPath2.0-Mods-metabolomics (2)

Thumb
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: 2017-12-19

Credits: User Thomas Duigou Network-member BioRetroSynth

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

Uploader

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

Thumb
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: User Thomas Duigou Network-member BioRetroSynth

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

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/1064


Alternative Formats

HTML
RDF
XML