Tag Results

Items tagged with "metabolic engineering" (7)

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

Files (1)

Uploader

Pablo Carbonell

View

Download

Pathway example for Selenzyme

Created: 2017-08-18 08:35:57 | Last updated: 2017-08-23 11:13:20

Credits: Pablo Carbonell

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Example of an input file containing information about a metabolic pathway to query the KNIME workflow for Selenzyme, an enzyme selection tool for pathway design.The file contains a list of reactions or generic reactions expressed in SMILES or SMARTS (SMIRKS) format. In the example, the list of reactions correspond to the different steps of a biosynthetic pathway.

File type: text/csv

Comments: 0 | Viewed: 36 times | Downloaded: 12 times

Tags:

Groups (1)

Owner

Thomas Duigou

View

BioRetroSynth

Unique name: BioRetroSynth
Created: Wednesday 24 May 2017 12:13:13 (UTC)

No description

21 shared items | 0 announcements

Members (3):

Tags:

Packs (1)

Creator

Pablo Carbonell

View

Download

Selenzyme

Created: 2017-08-18 08:23:47 | Last updated: 2017-08-23 11:12:00

Enzyme selection workflow for pathway design

2 items in this pack

Comments: 0 | Viewed: 40 times | Downloaded: 19 times

Tags:

Workflows (4)

KNIME

Uploader

Thomas Duigou

RetroPath2.0 - a retrosynthesis workflow w... (15)

Download

The RetroPath2.0 workflow build a reaction network from a set of source compounds to a set of sink compounds.When applied in a retrosynthetic fashion, the source is composed of the target compounds and the sink is composed of the available reactants (for instance in the context of metabolic engineering the sink is the set of native metabolites of a chassis strain). From amongst all the chemical reactions generated using RetroPath2.0 (in the retrosynthetic way), only a subset may effectively l...

Created: 2017-05-24 | Last updated: 2022-02-24

Credits: Thomas Duigou Baudoin Delépine BioRetroSynth

KNIME

Uploader

Pablo Carbonell

Workflow for Selenzyme v 1.0 (2)

Download

No description

Created: 2017-08-18 | Last updated: 2017-09-08

Credits: Pablo Carbonell

KNIME

Uploader

Pablo Carbonell

KNIME Workflow for RetroRules and Selenzyme (4)

Download

KNIME Workflow for RetroRules and SelenzymeThis worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction and selecting enzyme sequences using the Selenzyme tool.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Each reaction rule queries Selenzyem and outputs the selected Uniprot sequences for each rule.4. Resulting list of selected...

Created: 2018-07-24 | Last updated: 2018-08-11

Credits: Pablo Carbonell

KNIME

Uploader

Pablo Carbonell

KNIME Workflow for RetroRules and Retropat... (3)

Download

KNIME Workflow for RetroRules and RetroPath2.0This worflow provides an examples of retrieving the RetroRules reaction rules for some given reaction identifiers.1. Input to the workflow: Chemical reactions expressed using public database identifiers.2. Each reaction queries RetroRules and outputs the corresponding reaction rules.3. Resulting list of rulesenzymes is stored in a csv file in RetroPath2.0 format.Installation notesThe workflow runs a Python scrpt that requires pandas: Python Data A...

Created: 2018-07-26 | Last updated: 2018-08-11

Credits: Pablo Carbonell

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/5885

Alternative Formats