Table 1: Computation times (in s) for different methods. ( from [32].)

PDB code No. atoms LSMS PyMol Swiss-PDBV Chimera MSMS

1A8R 26400 0.65 2.61 5.56 10.52 6.38 16.36 0.95
1H2I 32318 0.72 1.83 6.50 11.37 5.25 40.04 3.03
1GTP 34740 0.51 2.20 6.98 13.15 4.75 67.04 9.02
1FKA 34977 0.75 2.77 7.89 26.29 7.36 77.25 4.50
1GT7 42700 0.95 2.43 7.32 16.10 6.50 54.39 3.32
1GAV 43335 0.55 2.54 7.05 28.86 7.71 78.35 4.22
1G3I 45528 0.54 2.85 8.18 19.45 6.21 7.67
1PMA 45892 0.40 1.97 8.23 18.67 6.72 12.90
1FJG 51995 0.71 2.88 8.01 25.18 8.05 15.11
1AON 58870 0.62 2.64 8.83 26.36 8.91 10.87
1J0B 60144 0.69 3.07 6.87 32.66 7.92 5.61
1OTZ 68620 0.67 2.28 8.46 30.14 9.56 9.03
1IR2 77088 0.65 2.88 7.09 29.31 9.55 93.87 9.49