Protex
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1) Introduction
2) About Protex
3) What are the license terms for using Protex?
4) Downloads and home page
5) How do I install this application?
6) Contact us

Introduction
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In 1962 Max F. Perutz won the Nobel Prize in Chemistry for deducing the structure of haemoglobin from data collected with x-ray crystallography. Today virtual laboratories use supercomputers and computer grids to solve protein structure problems by working from first chemical principles There are nice discussions at Stanford's folding@home page and at the Blueprint project's protein folding page. Each of these sites offers you the chance to enlist your own home computer in the protein folding task. (Also see http://www.technologyreview.com/articles/waldrop0502.asp.) 

About Protex 
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Protex is a part of MGX project developed by a team of graduate students (04-05) from the Department of Computer Science at UMass Boston. Protex stands for Protein Explorer. 

Protex is heavily based on the code written by Prof. Ethan Bolker for protein folding. Thanks to Prof. Bolker for great assistance with the protein folding code. 

Protex allows the beginning biology students to visualize protein folding and post-transactional modifications. Protex will mainly be used to teach the beginning biology students the fact that changing a single amino acid in a protein can dramatically alter its shape, and hence its biologicial activity. 

We model an amino acid as a disk (or sphere) of fixed radius with a hydrophobic index that describes how much an acid wants (index < 0) or does not want (index > 0) to be exposed to its watery environment. We imagine that the disks can occupy the cells of a regular tessellation of the plane (or space). A chain of amino acids folds so as to occupy a sequence of cells each sharing an edge (or face) with the next, in such a way as to minimize the energy, measured as the total number of edges (or faces) of occupied cells exposed to the environment (unoccupied cells), weighted by the hydrophobic indices of the amino acids occupying the cells. 


What are the license terms for using Protex? 
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This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. 
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 


Downloads and home page 
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The homepage is: <URL:http://www.cs.umb.edu/mgx/> 

Downloads of the current alpha release are available at: 
<URL:http://www.cs.umb.edu/mgx/alpha_release.htm> under Protex column 

 
How do I install this application? 
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Please see the INSTALL notes under Protex column. 


Contact us: 
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Feel free to send us feedback by email mgx@cs.umb.edu