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. 2006 Feb 10;90(9):3029–3042. doi: 10.1529/biophysj.105.076737

TABLE 1.

Association energies from FIRST and VIPER

Interface Symmetry Inline graphic VIPER (kcal/mol) Inline graphic FIRST (kcal/mol)
1–6 Quasi-fivefold −21.0 −9.0
1–38 Quasi-fivefold −21.0 −9.0
1–37 Quasi-twofold −29.0 −48.7
1–2 Quasi-threefold −33.0 −24.7
1–3 Quasi-threefold −33.0 −24.7

A comparison of the association energies for the Satellite Panicum Mosaic Virus (SPMV, PDB code 1stm) computed using VIPER 26 and with FIRST with Ecut = −0.7 kcal/mol. The interfaces are shown in Fig. 1 a. Note that in the simulations these energies are multiplied by the water shielding factor w = 0.17 to account for protein hydration.