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.