1. Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches 
Michael S. Lee, Mark A. Olson 
Biophysical Journal 
Volume 90, Issue 3, Pages (February 2006)
DOI: /biophysj
Copyright © 2006 The Biophysical Society Terms and Conditions

2. Figure 1
One-dimensional potential of mean force for pulling BUQ out of the FKBP binding pocket using GB-SA and hybrid explicit/implicit solvent models. See Theory and Methods sections for simulation details. Solid line indicates a hybrid solvent and dashed line signifies GB-SA implicit solvent. Arbitrary vertical shifts of each curve were manually adjusted so that the perceived asymptotic values of the PMF are located near 0.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2006 The Biophysical Society Terms and Conditions

3. Figure 2
One-dimensional potential of mean force for pulling FK506 out of the FKBP binding pocket using GB-SA and hybrid solvent models. See Fig. 1 for legend and details.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2006 The Biophysical Society Terms and Conditions

4. Figure 3
Distribution of modes for normal mode and quasiharmonic vibration calculations for the FKBP-BUQ complex. Harmonic modes (thin line) are shown for one complex structure from the RD4 calculation. Quasiharmonic modes (thick line) were obtained from the 1.5-ns production run of the GB-SA complex simulation. Frequency bins start at 1cm−1 and exponentially increase with a multiplier of 1.1.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2006 The Biophysical Society Terms and Conditions

5. Figure 4
Contribution to free entropy values from harmonic/quasiharmonic modes. See Fig. 3 for legend and details.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2006 The Biophysical Society Terms and Conditions