Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
Fig 7
Comparison of the accuracy of predicting side chains as well as cpu running time.
For all programs, time spent reading the protein structure and writing the results is excluded from the running time to focus on the cost of solving for the side chain positions. For Upside (10 Å cutoff), all side chain interactions with backbone or other side chains are cutoff at 10 Å.