MetaPrint2D in Bioclipse

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MetaPrint2D in Bioclipse

MetaPrint2D is a tool to predict metabolic sites in chemical structures based on historic metabolic data, described by circular fingerprints. If you use MetaPrint2D in Bioclipse, please cite:

Lars Carlsson, Ola Spjuth, Samuel Adams, Robert Glenn, Scott BoyerUse of Historic Metabolic Biotransformation Data as a Means of Anticipating Metabolic Sites Using MetaPrint2D and BioclipseBMC Bioinformatics 2010, 11:362    doi:10.1186/1471-2105-11-362

 

Installation

Install the latest Bioclipse available from Sourceforge. Go to menu "Help > Software Updates" and expand the Bioclipse Update site to reveal MetaPrint2D, check the box, and press Finish. After downloading and restarting, you now have the MetaPrint2D feature for Bioclipse installed.

 

Getting started

a) Single molecules

Open a molecular file in the the JChemPaint 2D-editor. Click one of the buttons in the MetaPrint2D toolbar to invoke the calculation and visualize the results in the editor. Hover over an atom to see more detailed information.

 

b) Multiple molecules

Open an SDF in the Molecules table and click the toolbar.

 

c) Scripting MetaPrint2D

A sample script is available as gist: http://gist.github.com/170410

 

d) More information

Open the Bioclipse help system and locate the topic for MetaPrint2D for more information and help about using the plugin. Also see the MetaPrint2D project site for details and source code of the MetaPrint2D implementation.

 

Project details

The MetaPrint2D plugin was written by Ola Spjuth at the department of Pharmaceutical Biosciences, Uppsala University, Sweden. Design and testing was done by Lars Carlsson at AstraZeneca, Mölndal, Sweden.

MetaPrint2D was written by Samuel Adams, based on a previous implementation of Lars Carlsson.

 

* License: Eclipse Public License (EPL)

* Source code is available from the git repository: http://github.com/bioclipse/bioclipse.metaprint2d

 

Support

* Mailing list: Please use the mailinglist bioclipse-users for questions regarding using MetaPrint2D. For developmental questions and feedback, please use the mailinglist bioclipse-devel.

* Bugs: Please report bugs using the Bioclipse Bugzilla available at http://bugs.bioclipse.net and please use the product 'Bioclipse2' and component 'MetaPrint2D'.