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Items tagged with "chemistry" (16)

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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


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



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


Workflows (13)

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 Automatic Protein-Ligand Docking (1)

Nimrod harnesses grid-based high-performance computing resources to evaluate a n umber of protein-ligand interaction algorithms. Different computational chemistry approaches are combined with non-linear optimization algorithms. This work is explained in Abramson, D. A., Amoreira, C., Baldridge, K. K., Berstis, L., Kondrick, C., Peachey, T. C., 2006, "A flexible grid framework for automatic protein-ligand docking", Proceedings of the Second IEEE International Conference on e-Science...

Created: 2009-05-15 | Last updated: 2009-05-16

Credits: User Jeffersontan

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)

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

 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 Text-mining using OSCAR to obtain a list o... (1)

This service extracts chemical names from text and obtains identifiers for these names. It outputs a HTML string that can be opened in a browser providing a table of information and links to ChemSpider.Known issues - Character limit ~3000 - Unable to produce InChIs or CSID for some names - Error sometimes encountered when a trivial and systematic name for the same compound are used - Some issues with identifiers being recognised but not able to be processedrequires access ...

Created: 2013-04-18

Credits: User Michael Smith User Mark Borkum

Attributions: Workflow InChIToCSID

Workflow From molecule name to SMILE and InchI usin... (2)

From molecule name to smile and inchi using chemspider. If the name cannot be matched to a chemspider identifier, the molecule name will appear in the results with an empty line. The output is a tab separated file.

Created: 2013-05-21 | Last updated: 2013-05-21

Credits: User Luna De Ferrari

Workflow Find isotopes with a certain exact match (1)

This script lists all isotopes matching a certain exact mass (given a certain error) and outputs the symbol, atomic number, and exact match of the search hits.

Created: 2013-07-30 | Last updated: 2013-07-31

Credits: User Egon Willighagen


Workflow SAR by Rgroup decomposition (1)

This workflow showcases a simple way to use Rgroup decomposition for SAR analysis.Once R-groups are obtained for several sites on the Scaffold, molecular properties like logP, TPSA, number of heavy/hetero-atoms, various kinds of ring counts are calculated.While medicinal chemistry purists may decry calculating properties for fragments/R-groups, correlating these at each site with Ki (or activity) shows up interesting trends.It's immediately apparent if increasing logP at a given site incr...

Created: 2015-09-15

Credits: User Insilicoconsulting


Workflow Drug-Drug Networks using Matador-DrugBank ... (1)

These days, Networks of all kinds are all the rage! So here's a trickle contributing to the flood.The workflow generates a network based on Similarity between known drugs based on commonality of their "direct" drug target interactions.The workflow does not provide a comparison between Chemical similarity based network and one based on shared drug targets. It only provides the latter.Other nodes and interfaces to Cytoscape and exported csv can be used to further the network analy...

Created: 2015-09-17 | Last updated: 2015-09-17

Credits: User Insilicoconsulting

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