Bioclipse:”Open Source” Tutorial: Free software for molecular scientists, 3D chemical modeling
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Bioclipse:”Open Source” Tutorial: Free software for molecular scientists, 3D chemical modeling


Bioclipse: Free software for molecular scientists. Bioclipse is open source software that integrates
separate programs into a single interface that lets you:
edit two dimensional structures manipulate three dimensional models
and predict molecular behavior Initially, the workbench is empty. After installing
“sample data”, the “left navigator panel” will have files. Bioclipse can edit two dimensional structures
using JChemPaint. From the left navigator panel,
within the 2D structures folder: open “ATP dot mol” To” edit” the tri-phosphate bond to a
di-phosphate bond, from the top tool bar,
select the “eraser” and click to “erase” the terminal oxygen
and phosphorus atoms. Other tools let you add bonds and create new
structures. In addition to 2D structures, Bioclipse provides
3D modeling by integrating Jmol. From the left navigator’s 3D structures folder,
open “pentanal dot cml” To rotate the molecule, click and drag within
the view panel To zoom in and out, scroll the middle mouse
wheel. To measure a distance, double click () on
one atom, then click () on a second atom. To measure an angle, click () a third atom. Jmol provides additional visualizations.
From the left side navigator – PDB folder – open “one dee six six” dot PDB
From the top Jmol menu, select “biopolymer” and “Cartoon on” Bioclipse provides additional functionality
via plugins from the “Help () Software Updates” feature. For example, after installing Metaprint2D,
you can predict metabolic sites. Open “ATP dot mol” and
(in the upper tool bar) click the “Execute Metaprint2D” icon
The highlighted atoms indicate that the “terminal phosphate bonds” are the most likely to
be metabolized. Additional plug-ins address “toxicity”
and (“partition coeffficients” to predict bodily drug distribution.) Bioclipse integrates JChemPaint and Jmol for
two … and three dimensional molecular structures… with additional plugins to predict behavior. Bioclipse: Free software for molecular scientists.

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