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.

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Created: 28th Jun 2020 at 14:12

Last updated: 28th Jun 2020 at 14:12

Last used: 22nd Jul 2021 at 13:04

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