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Table 2 Analysis of conformations obtained by the branch-and-pruning algorithm on the three proteins targets: 2JMY, 2KXA and 2KSL

From: An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

Proteins 2JMY 2JMY_1 2JMY_2 2KXA 2KSL
Number of      
residues 15 15 15 24 51
Number of      
vertices 107 107 107 170 359
Definition      
of α helices 1-15 3-13 5-11 1-11, 13-23 4-11, 13-27,
      29-36, 41-50
Position      
tolerance (Å) 0.2 0.2 0.2 0.2 0.2
Angle      
tolerance (°) 2 2 2 4 4
b value 4 4 4 8 4
Number of      
long-range      
constraints 0 0 0 1 3
Number of saved      
conformations 1 10000 10000 10000 10000
Number of generated      
conformations 1 633,937 928,399 3,380,964 491,498
CPU time - 1 min 1 min 25 min 31 min
Number of violated      
constraints (> 1Å) 0 4.0 ± 2.1 11.6 ± 3.6 9.6 ± 2.9 12.8 ± 1.1
Maximum      
violation (Å) 0 3.3 ± 1.4 4.8 ± 0.7 3.7 ± 1.0 8.1 ± 0.6
Mininum RMSD      
from PDB structure (Å) 1.4 1.3 2.1 1.1 3.0
RMSD from PDB structure      
for minimum violated      
conformations (Å) 1.4 2.9 2.8 1.3 3.5
PROCHECK      
core residues (%) 100 65.7 ± 25.9 49.2 ± 7.6 60.4 ± 8.1 76.9 ± 2.4
allowed residues (%) 0 17.9 ± 9.7 40.9 ± 8.3 39.6 ± 8.0 21.3 ± 2.8
gen.allow. residues (%) 0 3.6 ± 4.8 9.9 ± 7.2 0.0 ± 0.0 1.9 ± 1.7
disall. residues (%) 0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0 0.0 ± 0.0
  1. 2JMY_1 and 2JMY_2 correspond to the target 2JMY with shorter definitions of α helices. The total number of generated conformations is given, along with the number conformations filtered according to RMSD values.