IntercalateIntercalate Docking Dataset
| PDBID | DNA Seq. | Intercalation site(s) | RCSB DNA | MD DNA | |||
| (5'-3') | 1 | 2 | RMSD of top pose(Å) | Best RMSD (among 10 poses) (Å) | RMSD of top pose(Å) | Best RMSD (among 10 poses) (Å) | |
| 3FT6 | 3FT6 | 1 | 2 | 0.1 | 0.1 (1) | 1.7 | 1.4 (4) |
| 224D | 224D | 1 | 5 | 0.1 | 0.1 (1) | 1.2 | 1.2 (1) |
| 282D | 282D | 1 | 5 | 0.2 | 0.1 (2) | 1 | 1.0 (1) |
| 258D | 258D | 3 | - | 0.2 | 0.1 (2) | 1.3 | 1.2 (8) |
| 1K9G | 1K9G | 1 | 5 | 0.3 | 0.2 (2) | 1.5 | 1.5 (1) |
| 2DES | 2DES | 1 | 5 | 0.2 | 0.1 (1) | 3.8 | 1.5 (4) |
| 1IMS | 1IMS | 1 | 5 | 3.1 | 0.7 (5) | 1.3 | 1.2 (6) |
| 1IMR | 1IMR | 1 | 5 | 0.2 | 0.1 (3) | 1.3 | 1.2 (4) |
| 276D | 276D | 1 | 5 | 3 | 0.4 (2) | 1.1 | 1.1 (5) |
| 1D15 | 1D15 | 1 | 5 | 0.3 | 0.3 (1) | 1.2 | 1.1 (2) |
| 482D | 482D | 1 | 5 | 0.1 | 0.1 (1) | 3.4 | 3.4 (1) |
| 1D38 | 1D38 | 1 | 5 | 0.4 | 0.4 (1) | 1.2 | 1.2 (2) |
| 1D12 | 1D12 | 1 | 5 | 0.5 | 0.4 (1) | 1.2 | 1.1 (2) |
| 1NAB | 1NAB | 1 | 5 | 0.3 | 0.3 (1) | 1.6 | 1.6 (1) |
| 110D | 110D | 1 | 5 | 0.2 | 0.2 (1) | 1.5 | 1.5 (1) |
| 1Z3F | 1Z3F | 1 | 5 | 0.5 | 0.1 (6) | 1.4 | 1.4 (8) |
| 1KCI | 1KCI | 1 | 5 | 2 | 0.2 (10) | 2.4 | 1.2 (2) |
| 152D | 152D | 1 | 5 | 1.9 | 1.8 (1) | 1.5 | 1.5 (9) |
| 1D10 | 1D10 | 1 | 5 | 1.9 | 0.3 (3) | 1.2 | 1.2 (4) |
| 1D37 | 1D37 | 1 | 5 | 0.5 | 0.3 (5) | 2.2 | 1.4 (8) |
| 1D54 | 1D54 | 1 | 5 | 0.2 | 0.1 (3) | 3.2 | 1.2 (4) |
| 1D58 | 1D58 | 1 | 5 | 0.4 | 0.1 (3) | 1.2 | 1.1 (2) |
| 1D67 | 1D67 | 1 | 5 | 0.1 | 0.1 (1) | 1.2 | 1.1 (6) |
| 1DA9 | 1DA9 | 1 | 5 | 0.1 | 0.1 (1) | 1.4 | 1.3 (2) |
| 1N37 | 1N37 | 1 | 5 | 0.2 | 0.2 (1) | 4 | 1.8 (8) |
| 1P20 | 1P20 | 4 | - | 0.3 | 0.3 (1) | 1.3 | 1.3 (1) |
| 1QCH | 1QCH | 1 | 5 | 0.2 | 0.1 (2) | 1.2 | 1.1 (3) |
| 1R68 | 1R68 | 2 | - | 0.2 | 0.1 (6) | 3.7 | 3.7 (1) |
| 215D | 215D | 1 | 5 | 0.5 | 0.4 (3) | 3 | 1.1 (2) |
| 234D | 234D | 1 | 5 | 0.1 | 0.1 (1) | 3.5 | 3.0 (5) |
| 2GB9 | 2GB9 | 1 | 5 | 2 | 0.1 (10) | 1.4 | 1.4 (2) |
| 385D | 385D | 1 | 5 | 3.2 | 3.0 (5) | 3.2 | 3.2 (1) |
| 386D | 386D | 1 | 5 | 0.3 | 0.1 (2) | 2 | 1.9 (6) |
| 465D | 465D | 1 | 5 | 1.5 | 0.1 (9) | 2 | 1.2 (2) |
| 235D | 235D | 1 | 5 | 3.4 | 0.3 (2) | 3.1 | 1.4 (4) |
| 236D | 236D | 1 | 5 | 0.4 | 0.4 (1) | 3 | 3.0 (2) |
| 245D | 245D | 1 | 5 | 0.1 | 0.1 (1) | 1.2 | 1.2 (1) |
| 182D | 182D | 1 | 5 | 0.1 | 0.1 (2) | 1.2 | 1.2 (1) |
| 198D | 198D | 1 | 5 | 0.2 | 0.2 (1) | 1.4 | 1.3 (4) |
| 151D | 151D | 1 | 5 | 1.8 | 1.8 (1) | 1.3 | 1.2 (2) |
| 1DA0 | 1DA0 | 1 | 5 | 2.8 | 2.7 (6) | 1.2 | 1.2 (3) |
| 1D11 | 1D11 | 1 | 5 | 0.3 | 0.3 (1) | 1.2 | 1.1 (8) |
| 2GJB | 2GJB | 1 | 5 | 0.2 | 0.2 (3) | 0.8 | 0.8 (1) |
| 452D | 452D | 1 | 5 | 0.1 | 0.1 (3) | 2.2 | 1.4 (6) |
| 1DL8 | 1DL8 | 1 | 5 | 1.5 | 1.4 (10) | 1.8 | 1.4 (2) |
| 288D | 288D | 1 | 5 | 3.1 | 0.4 (9) | 1.1 | 1.1 (1) |
| 1MNV | 1MNV | 3 | 6 | 0.4 | 0.3 (2) | 5.8 | 5.5 (4) |
| 1M69 | 1M69 | 1 | 5 | 0.2 | 0.1 (9) | 2.1 | 1.2 (9) |
| 1D36 | 1D36 | 1 | 5 | 0.3 | 0.1 (2) | 1.2 | 1.1 (2) |
| 1G3X | 1G3X | 1 | 5 | 0.1 | 0.1 (1) | 4.8 | 4.8 (1) |
| 1VTH | 1VTH | 1 | 5 | 0.3 | 0.2 (4) | 1.2 | 1.2 (1) |
| 1VTI | 1VTI | 1 | 5 | 0.4 | 0.3 (9) | 3 | 2.9 (2) |
| 1JHI | 1JHI | 1 | 5 | 2.5 | 2.5 (1) | 2.9 | 1.3 (6) |
| 1DSD | 1DSD | 3 | - | 0.5 | 0.4 (3) | 5.3 | 5.2 (4) |
| 1FJA | 1FJA | 4 | - | 6.1 | 0.4 (4) | 6.9 | 6.6 (2) |
| 1AGL | 1AGL | 2 | 4 | 0.3 | 0.1 (3) | 3 | 3.0 (1) |
| 4L5K | 4L5K | 1 | 5 | 0.7 | 0.7 (8) | 2 | 2.0 (1) |
| 1D14 | 1D14 | 1 | 5 | 1.8 | 1.7 (3) | - | - |
| 1D17 | 1D17 | 1 | 5 | 0.2 | 0.2 (3) | - | - |
| 1D22 | 1D22 | 1 | 5 | 2.6 | 0.2 (3) | - | - |
| 366D | 366D | 1 | 5 | 1.7 | 0.1 (3) | - | - |
| 278D | 278D | 1 | 5 | 2 | 1.8 (3) | - | - |
| 1D21 | 1D21 | 1 | 5 | 0.2 | 0.2 (1) | - | - |
| 308D | 308D | 1 | 5 | 2.9 | 0.5 (10) | - | - |
| 367D | 367D | 1 | 5 | 1.7 | 0.2 (3) | - | - |
Intercalate Scoring Dataset
| PDB ID | Name | DNA seq (5'-3') | Ligand | Ligand charge | Binding Energies(kcal/mol) | |||
| ΔG° pred | ΔG° exp | |||||||
| 3FT6 | proflavine | CGATCG | Proflavine | 0 | -6.92 | -7.1 | ||
| 152D | dauno | CGATCG | Daunomycin | 1 | -9.55 | -10.1 | ||
| 198D | idarubicin | CGATCG | Idarubicin | 1 | -8.95 | -7.85 | ||
| 1D12 | doxo | CGATCG | Doxorubicin | 1 | -9.56 | -9.9 | ||
| 1Z3F | ellipticine | CGATCG | Ellipticine | 1 | -7.88 | -7.52 | ||
| 182D | nogalamycin | TGATCA | Nogalamycin | 1 | -9.63 | -9.3 | ||
| - | san_CG | CGCGCGCGCG | Sanguinarine | 1 | -8.51 | -9.46 | ||
| - | san_AT | ATATATATAT | Sanguinarine | 1 | -8.42 | -9.36 | ||
| - | PrOPC | CGATCG | Propyl-OPC (PrOPC ) | 1 | -8.28 | -8.93 | ||
| - | MeOPC | CGATCG | Methyl-OPC (MeOPC ) | 1 | -8.1 | -8.82 | ||
| - | HOPC | CGATCG | Oxazolopyridocarbazole chromophore (HOPC ) | 1 | -8.76 | -9.05 | ||
| - | coral_GC | GCGCGCGCGC | Coralyne | 1 | -9.6 | -10.56 | ||
| - | chel_CG | CGCGCGCGCG | Chelerythrine | 1 | -8.58 | -8.57 | ||
| - | EtOPC | CGATCG | Ethyl-OPC (EtOPC ) | 1 | -8.76 | -8.773 | ||
| - | quina_CG | CGCGCGCGCG | Quinacrine | 2 | -7.86 | -9.05 | ||
| - | quina_TA | TATATATATA | Quinacrine | 2 | -7.98 | -8.86 | ||
| - | harma_AT | ATATATATAT | Harmalol | 1 | -7.3 | -7.74 | ||
| - | harma_AA | AAAAAAAAAA | Harmalol | 1 | -7.04 | -7.51 | ||
| - | EB_GG | GGGGGGGGGG | Ethidium Bromide | 1 | -7.86 | -7.98 | ||
| - | thio_AT | ATATATATAT | Thionine | 1 | -7.01 | -6.95 | ||
| - | psf_GC | GCGCGCGCGC | Phenosafranine | 1 | -7.63 | -7.54 | ||
| - | psf_AT | ATATATATAT | Phenosafranine | 1 | -7.26 | -7.23 | ||
| - | EB_AA | AAAAAAAAAA | Ethidium Bromide | 1 | -7.55 | -7.78 | ||
| - | harma_GG | GGGGGGGGGG | Harmalol | 1 | -6.9 | -7.33 | ||
| - | psf_GG | GGGGGGGGGG | Phenosafranine | 1 | -7.5 | -7.48 | ||
| - | saf_GG | GGGGGGGGGG | Safranine-O | 1 | -7.6 | -7.17 | ||
| - | quina_GG | GGGGGGGGGG | Quinacrine | 2 | -7.75 | -8.16 | ||
| - | MB_CG | CGCGCGCGCG | Methylene Blue | 1 | -8.41 | -8.19 | ||
| - | coral_GG | GGGGGGGGGG | Coralyne | 1 | -8.83 | -8.8 | ||
| - | NME | CGATCG | 2-N methyl ellipticinium (NME) | 1 | -8.33 | -8.37 | ||
| - | 9MeE | CGATCG | 9-methoxy ellipticine (9meE) | 0 | -8.17 | -8.22 | ||
| - | saf_GC | GCGCGCGCGC | Safranine-O | 1 | -7.49 | -7.35 | ||
| - | quina_AA | AAAAAAAAAA | Quinacrine | 2 | -8.04 | -8.14 | ||
| - | MB_AA | AAAAAAAAAA | Methylene Blue | 1 | -7.82 | -7.56 | ||
| - | saf_AT | ATATATATAT | Safranine-O | 1 | -7.41 | -7.05 | ||
| - | san_GG | GGGGGGGGGG | Sanguinarine | 1 | -8.28 | -7.9 | ||
| - | chel_AA | AAAAAAAAAA | Chelerythrine | 1 | -8.52 | -8.24 | ||
| - | mtx | CTCGAG | Mitoxantrone | 0 | -8.75 | -8.38 | ||
| - | 9dd | CGATCG | 9-deoxydoxorubicin | 1 | -8.51 | -8.8 | ||
| - | thio_GC | GCGCGCGCGC | Thionine | 1 | -7.39 | -7.9 | ||
| - | thio_GG | GGGGGGGGGG | Thionine | 1 | -7.02 | -7.74 | ||
| - | adron_CG | CGATCG | Adriamycinone | 0 | -7.2 | -6.3 | ||
| - | san_AA | AAAAAAAAAA | Sanguinarine | 1 | -8.54 | -7.9 | ||