1. Use of Decoys to Optimize an All-Atom Force Field Including Hydration
Yelena A. Arnautova, Harold A. Scheraga 
Biophysical Journal 
Volume 95, Issue 5, Pages (September 2008)
DOI: /biophysj
Copyright © 2008 The Biophysical Society Terms and Conditions

2. Figure 1
Functional groups used in the OONS (34) solvent-accessible SA model.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

3. Figure 2 Flowchart of the parameter-optimization method.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

4. Figure 3
Scatter plot of the structures obtained by local minimization of the energies of the decoys from the training set with the original ECEPP05/OONS force field versus all-heavy-atom RMSDs from the experimentally determined native structure. (a) 1e0l. (b) 1gab. (c) 1igd. (d) 1l2y. (e) 1csp. (f) 1msi.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

5. Figure 4
Optimized values of the solvation parameters (σ) as a function of the size of a training set. The zero in the number of proteins indicates that the values of σ are the initial OONS (34) values.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

6. Figure 5
Scatter plot of the ECEPP05/SA energy (after parameter optimization) of the decoys from the training set versus the RMSD from the experimentally determined native structure. (a) 1e0l. (b) 1gab. (c) 1igd. (d) 1l2y. (e) 1csp. (f) 1msi. Red and blue circles correspond to the results obtained from either local energy minimization, or MCSA runs after local energy minimization, respectively.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

7. Figure 6
Scatter plot of the ECEPP05/SA energy (after parameter optimization) versus RMSD from the experimentally determined native structure for the proteins from the test set: (a) 1bdd; (b) 1vii; (c) 1res; (d) 1fsd; (e) 1cc7; (f) 1ail. Red and blue circles correspond to results obtained from local energy minimization, and MCSA runs after local energy minimization, respectively.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

8. Figure 7
Overlay of the experimental structure (red) and the decoy with the lowest ECEPP05/SA energy (green) obtained by local energy minimization for (a) 1cc7, (b) 1bdd, and (c) 1fsd, with RMSDs from the native structure of 1.7, 3.9, and 3.8Å, respectively.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

9. Figure 8
Overlay of the experimental structure (red) and the decoy with the lowest ECEPP05/SA energy (green) obtained from the MCSA run for 1vii. The RMSD from the native structure is 5.5Å.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

10. Figure 9
Scatter plot of the ECEPP05/SA energy (after parameter optimization) versus RMSD from the experimentally determined native structure for the proteins from the 4state-reduced set: (a) 1ctf, (b) 1r69, and (c) 2cro. Green, red, and blue circles correspond to results obtained from energy evaluation of fixed conformations, local energy minimization, and MCSA runs after local energy minimization, respectively.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions