Table 4. Testing results of the 5 real proteins.
R1, R2/R1, dRMSDT and dSE are the mean value calculated based on 3 trajectories in the backward MD and MD-MC simulations for three peptides, while they are from single trajectory for ubiquitin and cytochrome C. The representations of R1, R2, dSE are presented in Table 2. dRMSDT represents the reduction of RMSDT for hybrid MD-MC simulations as comparing to the parallel MD simulations. The hybrid MD-MC simulations with improvement in either SE or RMSD are bolded.
| protein | Target PDB | No. of residues | R1 (Å) | R2/R1 | dRMSDT (Å) | dSE | |
|---|---|---|---|---|---|---|---|
| MD | MD-MC | ||||||
| bovine antimicrobial peptide | 1G89 | 14 | 6.43 | 1.18 | 1.14 | -0.60 | 0.33 |
| arenicin-2 | 2JNI | 21 | 14.01 | 0.63 | 0.58 | 1.35 | -0.31 |
| magainin 2 | 4MGP | 23 | 2.36 | 1.38 | 1.19 | -2.98 | 0.68 |
| Ubiquitinǂ | 1UBQ | 76 | 2.77 | 1.80 | 1.20 | -2.67 | 0.95 |
| Ubiquitin* | 1.13 | -3.37 | 0.99 | ||||
| cytochrome Cǂ | 1HRC | 104 | 3.15 | 1.74 | 1.35 | -0.47 | 0.00 |
| cytochrome C* | 1.73 | 0.78 | 0.00 | ||||
ǂThe SAXS intensity profiles are from direct calculation without the consideration of experimental errors and hydration layer
*The SAXS intensity profiles are from experiments.