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i3Drefine : Software for protein 3D structure refinement

Purpose  :  Consistent and computationally efficient protein structure refinement

Project Website : http://protein.rnet.missouri.edu/i3drefine/

References :

(1)Bhattacharya. D, Cheng. J.i3Drefine software for protein 3D structure 
refinement. (submitted)

(2)D. Bhattacharya, J. Cheng.  3Drefine: Consistent protein structure refinement 
by optimizing hydrogen bonding network and atomic-level energy minimization.
Proteins: Structure, Function, and Bioinformatics 81(1):119-31, 2013

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Developed By: 

Debswapna Bhattacharya
Department of Computer Science
University of Missouri, Columbia
Email: db279@mail.missouri.edu

Contact:

Prof. Jianlin Cheng
Department of Computer Science
Informatics Institute
University of Missouri, Columbia
Email: chengji@missouri.edu

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1. INSTALLATION OF i3Drefine (Tested on Redhat Linux) 
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i3Drefine requires a java already installed in your system and you have already
downloaded the DSSP program (For detailed instruction, check the User Manual).

1) unzip the tarball 
   e.g. gunzip i3Drefine.tar.gz
        tar xzf i3Drefine.tar

2) change the directory to unzipped i3Drefine root directory 
   e.g. cd /home/your_home_dir/i3Drefine

3) Download DSSP and remane the executable to dssp and place it in: 
   e.g. cd /home/your_home_dir/i3Drefine/

4) setup environment vatiables (possibly addded to .bashrc file)

   e.g. export PATH=$PATH:/home/your_home_dir/jdk1.7.0_01/bin
        export CLASSPATH=$CLASSPATH:/home/your_home_dir/i3Drefine/software/3Drefine
        export CLASSPATH=$CLASSPATH:/home/your_home_dir/i3Drefine/software/3Drefine/programs

5) execute configure.pl from the root dir of i3Drefine to configure and 
   install the package:
   e.g. ./configure.pl

   Installaltion is done!

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3. USING i3Drefine
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i3Drefine needs two parameters as input: starting structure and number of refined
models to be produced. The interface program for refinement is located at
/home/your_home_dir/i3Drefine/bin/i3Drefine.sh

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4. TESTING OF i3Drefine
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1) refine target start_model (initial model is start_model.pdb)
   cd test
   ../bin/i3Drefine.sh start_model.pdb 5

   Refined structures are produced !

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5. RELEASE NOTES
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Version                  Reased On                    Comments
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1.0                     March 2013                 First released version       