Galaxy Retropath2.0
Version 1

This tool performs retrosynthesis search for possible metabolic routes between a source molecule and a collection of sink molecules. It takes as input, files from RetroRules, source and sink compounds (can be generated as explained in SynBioCAD Utilities), and the maximal pathway length (i.e; the number of steps). Only a single source molecule is processed at this time. Using Advanced Options, you can define the maximum number of compounds to keep for a next iteration (TopX), the minimal (dmin) and maximal (dmax) diameter for the reaction rules, and the maximum molecular weight of the source. The Server URL is the IP address of the tools. By default, a local address is mentioned but external servers may be specified here too. Lastly, the Timeout parameter can be used to increase the maximum execution time of the tool. This limit is set for the server version of the tool. Another internal limit is set for the RAM usage upon deployment. This is designed to limit the potential combinatorial explosion that may occur with RetroPath2.0 and enable the tool to be deployed on a server for numerous users to access it simultaneously.

help Creators and Submitter

Views: 478

Created: 28th Jun 2020 at 14:12

Last updated: 28th Jun 2020 at 14:12

Last used: 1st Jul 2022 at 14:36

help Attributions


Version History

Version 1 Created 28th Jun 2020 at 14:12 by Melchior du Lac

No revision comments

Related items

Powered by
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH
IBISBA is a pan-European research infrastructure that is currently funded by the EU Horizon 2020 projects
IBISBA 1.0 (grant agreement number 730976) and PREP-IBISBA (grant agreement number 871118).
Registering data or other knowledge assets on this platform is the sole responsibility of Users.
IBISBA cannot be held responsible for misuse or misappropriation of data and assets belonging to a Third Party..

By continuing to use this site you agree to the use of cookies