Table S1.
Binding pocket analysis for initial and MD-BSA using DoGSiteScorer
| Structure | nb | Pocketc | Volume (Å3) | Surface (Å2) | Liposurface (Å2) | Depth (Å2) |
|---|---|---|---|---|---|---|
| Initial-BSA | 15 | 1 | 979.56 | 1,208.59 | 792.46 | 33.22 |
| 2 | 972.45 | 1,175.37 | 870.87 | 26.29 | ||
| 3 | 910.76 | 1,086.47 | 686.13 | 21.3 | ||
| MD-BSAa | 18 | 1 | 996.04 | 1,318.51 | 859.25 | 24.55 |
| 2 | 905.07 | 1,049.02 | 824.14 | 24.67 | ||
| 3 | 904.64 | 1,080.84 | 808.19 | 26.48 |
Notes:
a
BSA after 5 ns MD simulation;
b
number of BSA potential binding pockets;
c
main binding pockets based on the algorithm of DoGSiteScorer. Major structural features analyzed were pocket volume, solvent-accessible surface, liposurface, and pocket depth.
Abbreviations: MD, molecular dynamics; BSA, bovine serum albumin.