Workflows

Search filter terms
Filter by type
Filter by tag
Filter by user
Filter by licence
Filter by group
Results per page:
Sort by:
Showing 65 results. Use the filters on the left and the search box below to refine the results.
Type: KNIME
Uploader

Workflow RDKit Aggregator Advisor (1)

Thumb
A Knime (2.12.1) workflow that uses RDKit nodes for assessing the risk of a compound to form aggregates under biochemical assay conditions, inspired by the Aggregation Advisor paper of Irwin et al. While the Aggregator Advisor web tool allows for aggregation risk assessment of individual compounds, this Knime workflow can be used to quickly run through large compound collections.Query structures are loaded as an SD file (here a set of 1090 approved drugs), and are then compared for Tanimoto s...

Created: 2015-10-18 | Last updated: 2015-10-18

Credits: User Evert Homan

Uploader

Workflow RDKit PAINS 4 (1)

Thumb
Improved Knime (2.12.1) workflow for detection of Pan-Assay Interference Compounds (PAINS) using RDKit nodes. PAINS SMARTS curated by Greg Landrum are used for the substructure searches. These yield 753 hits among the WEHI set of 10,000 compounds. A Total Hits count column is added by the RDKit Substructure Counter node, so no additional aggregation is needed. Structures devoid of PAINS are separated out for further progression, while the PAINS hits can be visually inspected using the RDKit I...

Created: 2015-10-18 | Last updated: 2015-10-18

Credits: User Evert Homan

Uploader

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

Thumb
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

Uploader

Workflow SAR by Rgroup decomposition (1)

Thumb
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 Answer to biostar https://www.biostars.org... (1)

Thumb
My answer to https://www.biostars.org/p/138848/ Question: How to replace a set of sequence ID's with another set of sequence ID's ?? Let us consider I have a file (Notepad or MS-doc) having 10 sequences with ID's A, B, C, D, E, F, G, H, I, J. I want to replace the ID's with K, L, M, N, O ,P, Q, R, S, T i.e., A to re replaced with K, B to be replaced with M and so on. How can I do this? I am a Biologist who have newly started analyzing Large data's and having this prob...

Created: 2015-04-20 | Last updated: 2015-04-20

Credits: User Pierre Lindenbaum

Workflow Q4: For a given interaction profile, give ... (1)

Thumb
In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Compound Information followed by Compound Information (Batch) followed by Chemical Structure Search: Similarity with filter search...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q19: For the targets in a given pathway, r... (1)

Thumb
In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Pathway Information: Get Targets followed by Target Pharmacology with filter minEx-pChembl=5 to answer scientific competency quest...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q18:For pathway X, find compounds that ago... (1)

Thumb
In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Pathway Information: Get Targets followed byTarget Pharmacology with filters activity_type=Potency, max-activity_value=1000, activ...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q16:Targets in Parkinson's disease or Alzh... (1)

Thumb
In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call Target for Disease followed by Target Pharmacology with filter minEx-pChembl=5 to answer scientific competency question Q16:Target...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Workflow Q15: a) Which chemical series have been sh... (1)

Thumb
In the Open PHACTS project, we have developed KNIME utility nodes that can be set to automatically leverage the desired content from Open PHACTS web services and simplify the construction of workflow processes.  In this workflow we use the these KNIME nodes (which can be down loaded here: https://github.com/openphacts/OPS-Knime ) with the Open PHACTS API call a) Classification of Compounds for Target with filter minEx-pChembl=5 and b) Associations for Disease to answer scientif...

Created: 2014-10-22

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Results per page:
Sort by: