HomeGroupPublicationsResourcesContact Us Back to Preddicta DNA DRUG COMPLEX DATA SET PreDDICTA is validated on the following dataset of DNA-drug complexes consisting of 16 minimized crystal structures and 34 model-built structures. The model built structures have also been deposited at RCSB and the PDB IDs of all files is provided below. Each structure can be downloaded by clicking on its PDB ID given below. The following table lists the experimental binding affinity data obtained from literature and the predicted binding free energies, ΔGo and ΔTm using both, the approximate charge method (option 1) and accurate charge method (option2). Formal drug charge required for option 2 is listed in column 5. Option 1:           Option 2: Formal Drug Charge: -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 E-mail  S.No. Complex Drug description DNAa Drug charge Experimental  Option1 Predicted Option2 Predicted ΔGo ΔT m ΔGocbe ΔGopred ΔT mpred ΔGocbe ΔGopred ΔT mpred Minimized Crystal Structures 1 127DM Hoechst 33258 s1 + 1 -11.0 17.9 -26.0 -11.2 19.4 -27.5 -11.3 20.4 2 264DM Hoechst 33258 s2 + 1 -11.7 - -32.5 -12.0 23.8 -36.5 -12.5 26.6 3 109DM Bi-benzimidazole derivative s1 + 1 -12.0 23.9 -30.5 -11.7 22.5 -35.1 -12.3 25.5 4 2DBEM Berenil s1 + 2 -8.6 8.0b -4.9 -8.5 5.0 -5.9 -8.6 5.6 5 1D63M Berenil s2 + 2 -8.0 - -8.7 -9.0 7.6 -8.0 -8.9 7.1 6 121DM Netropsin s2 + 2 - 20.0 -22.2 -10.7 16.8 -20.3 -10.4 15.5 7 261DM Netropsin s3 + 2 -11.5c - -29.1 -11.5 21.5 -32.5 -12.0 23.8 8 2DNDM Distamycin s2 + 1 - 21.0 -28.9 -11.5 21.3 -30.7 -11.7 22.6 9 1JTLM Distamycin s4 + 1 -11.5d - -32.6 -12.0 23.9 -35.9 -12.4 26.1 10 227DM Bisfuramidine s1 + 2 -9.3 8.3 -5.2 -8.5 5.2 -7.9 -8.9 7.1 11 298DM Isopropyl bisfuramidine s1 + 2 - 14.4 -20.1 -10.4 15.3 -19.0 -10.3 14.6 12 289DM Cyclopropyl bisfuramidine s1 + 2 - 12.4 -17.4 -10.1 13.5 -17.3 -10.1 13.5 13 1FMQM Cyclobutyl bisfuramidine s1 + 2 - 14.8 -20.7 -10.5 15.8 -19.9 -10.4 15.2 14 1EELM Cyclopentyl bisfuramidine s1 + 2 - 15.8 -22.7 -10.7 17.1 -22.7 -10.7 17.1 15 1FMSM Cyclohexyl bisfuramidine s1 + 2 - 15.4 -26.2 -11.2 19.5 -24.3 -10.9 18.2 16 1PRPM Propamidine s1 + 2 -8.2 - -12.5 -9.4 10.2 -8.6 -9.0 7.5 Minimized Crystal Structures 17 2GXC Bisfuramidine s1 + 2 - 13.6 -22.6 -10.7 17.1 -22.6 -10.7 17.1 18 2GXD Bisfuramidine s1 + 2 - 9.1 -8.8 -9.0 7.7 -8.4 -8.9 7.4 19 2GXE Bisfuramidine s1 + 2 - 7.7 -14.0 -9.6 11.2 -14.2 -9.7 11.4 20 2GXH Bisfuramidine s1 + 2 - 10.9 -19.5 -10.3 14.9 -16.4 -9.9 12.9 21 2GXI Bisfuramidine s1 + 2 -8.5 - -11.7 -9.4 9.7 -9.5 -9.1 8.1 22 2GXJ Phenylbenzimidazole s1 + 1 -9.1 7.0 -3.7 -8.3 4.2 -5.1 -8.5 5.2 23 2GXK Phenylbenzimidazole s1 + 1 -9.0 6.2 -6.7 -8.7 6.2 -7.3 -8.8 6.7 24 2IRJ Phenylbenzimidazole s1 + 1 -8.6 4.9 -6.1 -8.6 5.8 -6.5 -8.7 6.1 25 2GXM Phenylbenzimidazole s1 + 1 -8.8 5.6 -7.7 -8.8 6.9 -8.0 -8.9 7.1 26 2GXN Phenylbenzimidazole s1 + 1 -9.2 7.5 -6.3 -8.7 6.0 -4.8 -8.5 4.9 27 2GXO Phenylbenzimidazole s1 + 1 -9.1 7.0 -3.2 -8.3 3.8 -4.2 -8.4 4.5 28 2GXP Phenylbenzimidazole s1 + 1 -9.1 7.0 -7.5 -8.8 6.8 -9.5 -9.1 8.1 29 2GXR Phenylbenzimidazole s1 + 2 -10.7 15.6 -18.6 -10.2 14.3 -18.9 -10.3 14.5 30 2GXT Phenylbenzimidazole s1 + 2 -10.9 17.1 -23.0 -10.8 17.3 -26.5 -11.2 19.7 31 2GXV Symmetric Bi-benzimidazole s1 + 2 -11.9 22.8 -15.4 -9.8 12.1 -22.1 -10.7 16.7 32 2IRK Symmetric Bi-benzimidazole s1 + 2 -8.1 2.8 2.3 -7.6 0.1 -0.8 -8.0 2.2 33 2GXX Symmetric Bi-benzimidazole s1 + 2 -8.1 2.8 0.0 -7.9 1.6 -0.1 -7.9 1.7 34 2GXY Symmetric Bi-benzimidazole s1 + 2 -10.7 15.9 -11.0 -9.3 9.1 -14.3 -9.7 11.4 35 2IRL Symmetric Bi-benzimidazole s1 + 2 -10.8 16.4 -21.5 -10.6 16.3 -23.8 -10.9 17.9 36 2GY0 Symmetric Bi-benzimidazole s1 + 2 -9.7 10.0 -8.2 -8.9 7.2 -9.5 -9.1 8.1 37 2GY1 Symmetric Bi-benzimidazole s1 + 2 -9.2 7.1 -9.1 -9.0 7.8 -8.8 -9.0 7.7 38 2GY2 Symmetric Bi-benzimidazole s1 + 2 -12.7 28.5 -35.1 -12.3 25.6 -39.0 -12.8 28.2 39 2GY3 Symmetric Bi-benzimidazole s1 + 2 -11.8 22.2 -34.8 -12.3 25.4 -34.8 -12.3 25.4 40 2GY4 Symmetric Bi-benzimidazole s1 + 2 -11.6 20.8 -30.0 -11.7 22.1 -28.7 -11.5 21.2 41 2GY6 Asymmetric Bi-benzimidazole s1 + 1 -11.9 23.0 -22.9 -10.8 17.3 -27.9 -11.4 20.7 42 2GY8 Asymmetric Bi-benzimidazole s1 + 1 -11.9 23.0 -23.9 -10.9 17.9 -28.5 -11.5 21.1 43 2GYE Asymmetric Bi-benzimidazole s1 + 1 -11.9 23.0 -25.4 -11.1 19.0 -30.6 -11.7 22.5 44 2GYF Asymmetric Bi-benzimidazole s1 + 1 -12.1 24.4 -31.4 -11.8 23.1 -35.7 -12.4 26.0 45 2GYG Asymmetric Bi-benzimidazole s1 + 1 -12.3 25.8 -33.2 -12.1 24.3 -37.6 -12.6 27.3 46 2GYH Asymmetric Bi-benzimidazole s1 + 1 -12.3 25.4 -29.0 -11.5 21.4 -34.0 -12.2 24.8 47 2GYJ Asymmetric Bi-benzimidazole s1 + 2 -13.0 30.1 -37.5 -12.6 27.2 -40.7 -13.0 29.4 48 2GYL Asymmetric Bi-benzimidazole s1 + 2 -13.1 30.7 -39.6 -12.9 28.6 -44.5 -13.5 32.0 49 2GYM Imidazole-Pyrrole Polyamide s5 + 1 -9.4 11.0 -16.2 -9.9 12.7 00.0 00.0 (-9.2e) 00.0 (8.8e) 50 2GYN Imidazole-Pyrrole Polyamide s6 + 1 -8.1 5.7 -13.8 -9.6 11.1 00.0 00.0 (-9.1e) 00.0 (8.5e) a Double stranded oligomers with sequences s1=CGCGAATTCGCG, s2= CGCAAATTTGCG, s3= CGCAATTGCG, s4= GGCCAATTGG, s5=GCCTGTTAGCG, s6= GCCTATTAGCG; b For GCAATTGC; c For CGCAAATTGGC; d For GCGAATTCGC; e Values obtained when the extended structure of the hairpin polyamide is used for accessible surface area calculation. Key: ΔGo Standard binding free energy ΔTm Change in melting temperature of DNA oligomer due to drug binding ΔGocbe Calculated binding energy estimated from energy function ΔGopred Predicted binding energy from ΔGocbe ΔTmpred Predicted ΔTm from ΔGocbe