Table 4 Complexes considered in the unbound docking experiment, for which GRAMM produced near-native structures, with their PDB and chain identifiers
From: DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
Recognition by DARS-RNP and QUASI-RNP | Molecule name | Complex PDB code | Receptor PDB code (and its RMSD vs the bound structure) | Ligand PDB code (and its RMSD vs the bound structure) |
|---|---|---|---|---|
| Â | Norwalk Virus polymerase with CTP/RNA primer | 3bso_a:p | 1sh0_b (1.3) | 3bso_p (0.0) |
Successful | HutP/Hut mRNA | 1wpu_a:c | 1wpv_a (0.2) | 1wpu_c (0.0) |
| Â | 9-subunit archaeal exosome/RNA | 2jea_a, b:c | 2je6_a, b (0.4) | 2jea_c (0.0) |
| Â | SRP 19/7S.S SRP RNA | 1lng_a:b | 1lng_a (0.0) | 1z43_a (2.1) |
| Â | Tyrosyl - tRNA synthetase splicing factor/group I intron RNA | 2rkj_b:c | 1y0q_a (3.0) | 1y42_x (0.9) |
Unsuccessful | SRP C-termina domain/4.5 S RNA | 2pxv_a:b | 1cql_a (8.1) | 2pxv_a (0.0) |
| Â | spliceosomal 15.5 K protein/U4 snRNA fragment | 1e7k_a:c | 2jnb_a (3.2) | 1e7k_c (0.0) |
| Â | Synthetic Fab/P4-P6 ribozyme domain | 2r8s_l, h:r | 1hr2_a (4.3) | 2r8s_l, h (0.0) |