RosettaDock 2.1
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Thank you for downloading the Rosetta Docking software!  To use:

1. If you have not already done so, install the packages
   rosetta_source, rosetta_documentation, and rosetta_database
   in one location.  Install RosettaDock in the same location

2. Run ./setup.sh to link rosetta components to this directory

3. Open ./documentation/tutorial/index.html in a web browser for complete
   instructions for running RosettaDock.

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References and authors:

Jeffrey J. Gray, Chu Wang, Ora Schueler-Furman, Michael Daily, Kurt
Pipenbrink, Brian Kuhlman, Carol Rohl, Kira Misura, Bill Schief, Tanja
Kortemme, David Baker 

Johns Hopkins University and University of Washington 2005

Please reference:

1. Gray, J.J., S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman,
   C.A. Rohl, D. Baker "Protein-Protein Docking with Simultaneous
   Optimization of Rigid-Body Displacement and Side-Chain
   Conformations".  J. Mol. Biol.  vol.331. 1 (2003). pp. 281 - 299.

2. Gray, J.J., S.E. Moughan, T. Kortemme, O. Schueler-Furman,
   K.M.S. Misura, A.V. Morozov, D. Baker "Protein-Protein Docking
   Predictions for the CAPRI Experiment".  Proteins.  vol.52. 1
   (2003). pp. 118 - 122.

3. Daily, M.D., D. Masica, A. Sivasubramanian, S. Somarouthu,
   J. J. Gray "CAPRI rounds 3-5 reveal promising successes and future
   challenges for RosettaDock".  Proteins. vol.60. 2 (2005). pp. 181-186.

4. C. Wang, O. Schueler-Furman and D. Baker "Improved side-chain
   modeling for protein-protein docking". Protein Science. vol. 14. 5.
   (2005). pp. 1328-1339.

5. O. Schueler-Furman, C. Wang and D. Baker "Progress in
   Protein-protein docking: Atomic Resolution Predictions in the CAPRI
   experiement using RosettaDock with an improved treatment of side
   chain flexibility". Proteins. vol.60. 2 (2005). pp. 187-194.

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Changes:

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What's new since RosettaDock 2.0:  [Release 2.1, August 2006]

1. Additional scripts for efficient global optimization protocol.

Scorefilters are defined that allow to create only low-energy decoys. This is
achieved by analyzing a short calibration docking run (typically 5000 decoys).
The script evaluates the enrichment in low-energy decoys that different energy filters would produce.

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What's new since RosettaDock 1.0:  [Release 2.0, May 2005]

1. Conversion of the code to C++
2. Addition of side-chain minimization routines [4,5]
3. Use of unbound rotamer conformations [4,5]
4. Scripts for creating antibody profiles
5. Tutorial
6. Automatic detection and protection of disulfide bonds via
   preprocessing scripts.
7. Additional sample scripts for perturbation and global runs,
   including condor scripts for running on a computing cluster.

