Table 1 Molprobity evaluation before and after 20 ns MD refinement of CCHFV-RdRp models created from different programs.

From: In silico structural elucidation of RNA-dependent RNA polymerase towards the identification of potential Crimean-Congo Hemorrhagic Fever Virus inhibitors

Programs implemented

Template

MP-score**

Clash-score*

Rot-out (%)

Rot-fav (%)

Ram-out (%)

Ram-fav (%)

before

after

before

after

before

after

before

after

before

after

before

after

I-TASSER

5amq.A

3.91

1.87 (82nd)

160.92

1.49 (99th)

5.64

3.31

85.33

89.92

4.26

2.06

86.23

88.68

LOMETS

5amq.A

3.7

1.79 (86th)

138.76

1.29 (99th)

5.33

2.45

84.99

87.76

4.16

2.95

88.13

86.01

RAPTORX

5amq.A

3.73

1.88 (81st)

138.6

1.55 (99th)

5.43

3.38

85.12

90.09

4.21

2.3

89.26

88.63

MUSTER

5amq.A

3.85

1.7 (89th)

150.44

1.16 (99th)

5.36

2.33

82.7

89.86

5.05

2.3

85.25

88.31

MODELLER+

5amq.A

3.4

1.44 (99th)

80.7

0.65 (99th)

4.29

1.82

86.04

90.4

3.42

1.68

90.16

91.89

  1. *Clash score is the number of serious steric overlaps (>0.4 Å) per 1000 atoms.
  2. **MolProbity score combines the clashscore, rotamer, and Ramachandran evaluations into a single score, normalized to be on the same scale as X-ray resolution. (100th percentile is the best among structures of comparable resolution; 0th percentile is the worst.
  3. +Final model by MODELLER was made using 5 amq.A as most fitted-template based on conserved structural attributes obtained from multiple 3D structural alignments of all models (built from other programs) with 5 amq.A.