Table 1.
Minimum backbone RMSD values of the loops sampled by five different algorithms.
Table 2.
Comparison of of the loop conformations sampled by DiSGro and six other methods using Test Set 2 used by Ref. [42].
Table 3.
Comparison of ,
and
of the lowest energy conformations of the loops sampled by RAPPER, FALCm4 and DiSGro using Test Set
.
Figure 1.
Top five lowest energy loops of length 12 for single-metal-substituted concanavalin A (pdb 1scs, residues 199–210).
The lowest energy loop after side-chain construction is colored in red, and the native structure is in white.
Table 4.
Comparison of accuracy of modeled loops using the original Fiser data set of loops with –
residues.
Table 5.
Comparison of of the loop conformations sampled by Loop Builder and DiSGro using Test Set 4 taken from the Loop Builder study [42].
Table 6.
Accuracy of modeled loops by DiSGro using the original Fiser data set of loops with 13 residues.
Table 7.
Comparison of ,
and
of the loop conformations sampled by PLOP and DiSGro using Test Set
.
Figure 2.
The time cost of energy calculations for generating one single loop.
(A) The plot of computing time versus protein size show a large time saving of “Redcell-On” (red solid curve) compared to “Redcell-Off” (black dashed curve) for 12-residue loops, and (B) The plot of 6-residue loops. (C) Plot of computing time versus protein size show “Redcell-On” (red solid curve) has significantly improved computational time cost compared to “Ellipsoid-Only” (black dashed curve) and “Cutoff-Only” (green solid curve).
Figure 3.
Schematic illustration of placing and
atoms.
Atom has to be on the circle
. The position
of the
atom of residue
is determined by
, which is based on known distance
and the conditional distribution of
. Once
is sampled,
can be placed on two positions with equal probabilities. Here
is the selected position of
.
(yellow ball) is placed at the position
alternative to
. Similarly, the
atom has to be on the circle
and its position
is determined by
in a similar fashion.
Figure 4.
Mean of minimum backbone RMSD values for protein loops.
We generated samples for each loop. The mean value of the minimum RMSD of the
loops (
-axis) is plotted against the size of trial samples
(
-axis) for different choices of
. For control, results obtained without sampling torsion angles (
, control) are also plotted. The backbone (N,
, C and O atoms) RMSD in this paper is calculated by fixing the rest of the protein body.
Figure 5.
Schematic illustration of ellipsoid criterion.
(A) Three dimensional view of a point locating on the ellipsoid constructed from the total loop length
and the two foci
and
. (B) Two dimensional view along through the
-axis of the ellipsoid, with
and
(dark gray).
is along
-axis, not shown. The maximum side-chain length is denoted as
and the distance cut-off of interaction is
. The enlarged ellipsoid, which has updated
and
, is also shown (light gray).