Table 2 Minimum RMSD (out of 1000 tries) between a fixed segment derived from a protein structure and a closed segment generated by FCCD. The length of the loops is shown between parentheses in the upper row.
From: Full cyclic coordinate descent: solving the protein loop closure problem in Cα space
Loop (4) | RMSD | Loop (8) | RMSD | Loop (12) | RMSD |
|---|---|---|---|---|---|
1dvj, A, 20–23 | 0.59 | 1cru, A, 85–92 | 2.31 | 1cru, A, 358–369 | 3.37 |
1dys, A, 47–50 | 0.67 | 1ctq, A, 144–151 | 2.22 | 1ctq, A, 26–37 | 2.40 |
1egu, A, 404–407 | 0.61 | 1d8w, A, 334–341 | 2.04 | 1d4o, A, 88–99 | 3.20 |
1ej0, A, 74–77 | 0.61 | 1ds1, A, 20–27 | 2.20 | 1d8w, A, 43–54 | 2.74 |
1i0h, A, 123–126 | 0.73 | 1gk8, A, 122–129 | 2.20 | 1ds1, A, 282–293 | 3.16 |
1id0, A, 405–408 | 0.66 | 1i0h, A, 145–152 | 2.42 | 1dys, A, 291–302 | 2.90 |
1qnr, A, 195–198 | 0.54 | 1ixh, 106–113 | 1.98 | 1egu, A, 508–519 | 3.06 |
1qop, A, 44–47 | 0.58 | 1lam, 420–427 | 2.16 | 1f74, A, 11–22 | 3.12 |
1tca, 95–98 | 0.76 | 1qop, B, 14–21 | 2.17 | 1q1w, A, 31–42 | 3.04 |
1thf, D, 121–124 | 0.56 | 3chb, D, 51–58 | 1.97 | 1qop, A, 175–186 | 2.97 |
Average RMSD | 0.63 | Average RMSD | 2.17 | Average RMSD | 3.00 |