RW potential mannual  
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A distance-dependent atomic potential from random-walk ideal chain reference state 
package version 1.0

1. Introduction.

   RW is distance-dependent atomic potential for protein structure modeling and structure 
   decoy recognition. It is calculated from 1,383 high-resolution PDB structures using an 
   ideal random-walk chain as the reference state. The RW potential has been extensively 
   optimized and tested on a variety of protein structure decoy sets and demonstrates a 
   significant power in protein structure recognition and a strong correlation with the 
   RMSD of decoys to the native structures. 
   

   The package includes following files:

       1) calRW   : The executable program to calculate RW score;
       2) data    : The RW potential data file;
       3) pro.pdb : The example pdb file;
       4) readme  : Readme file.

2. Installation.

   You need to download the "calRW.tar.gz" file and unpack the files by running "tar -xzf calRW.tar.gz".
   Have "calRW" and "data" files in the same folder.

3. Usage.

   ./calRW pdb
   Example: ./calRW pro.pdb
   Result should be: RW potential =   -17737.993352 kcal/mol   

4. Contact.

   For question and comments, please contact: 
   Jian Zhang (jianzha@umich.edu) or 
   Yang Zhang (zhng@umich.edu).

5. Reference.

   Please cite following paper when you use the RW potential:

   Jian Zhang, Yang Zhang. A Novel Side-Chain Orientation Dependent 
   Potential Derived from Random-Walk Reference State for Protein 
   Fold Selection and Structure Prediction. PLoS One, vol 5, e15386 (2010).