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

1. Introduction.

   RWplus is orientation-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) calRWplus   : The executable program to calculate RW score;
       2) rw.dat      : The RW potential data file;
       3) scb.dat     : The RW potential data file;
       4) pro.pdb     : The example pdb file;
       5) readme      : Readme file.

2. Installation.

   You need to download the "calRWplus.tar.gz" file and unpack the files by running "tar -xzf calRWplus.tar.gz".
   Have "calRWplus" and "rw.dat" and "scb.dat" files in the same folder.

3. Usage.

   Example: ./calRWplus pro.pdb
   Result should be: RW potential =   -18960.201548 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 RWplus potential:

   Jian Zhang and Yang Zhang, A Orientation-Dependent Atomic 
   Potential Derived from Random-Walk Ideal Chain Reference 
   State for Protein Fold Selection and Structure Prediction (2009) submitted.