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PDB ID Mentions in PubMed Central Article count: 1

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PDB ID Mentions in PubMed Central

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Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock.

(2009) J Cheminform 1

PubMed: 20150996 | PubMedCentral: PMC2820493 | DOI: 10.1186/1758-2946-1-15

PDB code of the complex RMSD of the first rank result as compared to the X-ray (Å) Energy rank of the lowest RMSD hit Frequency rank/frequency of the best geometry Lowest RMSD (Å) Esti... ated free energy of binding (kcal/mol) Experimental binding energy (kcal/mol) 1AI5 1.22 1 1/100 0.65 -5.06 -5.08 1AJP 2.73 2 1/97 1.07 -4.82 -3.05 1AMW 2.13 1 1/35 0.87 -5.67 -6.19 1BGQ 1.03 1 1/100 0.70 -6.50 -11.69 1CBR 1.01 1 1/93 0.77 -7.42 -10.58 1D3Q 2.77 2 2/40 0.85 -11.47 -8.88 1D3T 2.09 3 1/60 0.99 -10.37 -8.73 1DWB 0.72 1 1/100 0.54 -4.87 -3.98 1FLR 0.39 1 1/100 0.39 -8.54 -10.98 1GNI 3.01 2 1/69 1.01 -6.80 -11.01 1HVJ 1.61 1 1/5 1.61 -10.45 -14.27 1HVR 1.21 1 1/96 1.00 -11.67 -12.97 1K4G 2.83 4 1/89 1.42 -7.78 -7.99 1KV1 0.6 1 1/100 0.58 -9.33 -8.10 1LIF 3.1 4 3/17 0.93 -4.51 -9.65 1M0N 1.18 1 1/86 1.02 -7.65 -3.03 1M0Q 1.03 1 1/80 0.95 -7.15 -5.30 1OLU 0.89 1 1/89 0.61 -9.14 -6.01 1Q8T 1.9 1 1/100 1.41 -7.58 -6.49 1RBP 0.85 1 1/100 0.56 -8.46 -9.17 1S39 4.29 2 1/95 0.33 -4.65 -10.50 1U33 0.86 1 1/43 0.80 -9.82 -6.28 1ULB 0.7 1 1/100 0.64 -5.09 -7.20 1UWT 2.35 1 1/53 0.71 -6.47 -8.14 1X8R 1.26 1 1/100 0.96 -3.10 -8.36 1XD1 1.81 1 2/10 1.30 -15.97 -10.80 1YDT 0.79 1 1/93 0.45 -8.05 -9.98 1ZC9 2.7 14 2/26 0.96 -6.76 -4.39 2ACK 3.98 4 2/22 0.94 -5.25 -8.97 2BAJ 0.66 1 1/100 0.55 -12.50 -11.46 2BAK 1.21 1 1/98 0.64 -14.20 -10.14 2CEQ 0.85 1 1/44 0.83 -6.23 -9.92 2CET 2.61 1 2/15 0.96 -7.76 -10.94 2CGR 0.9 1 1/100 0.68 -10.05 -9.89 2CPP 1.21 1 1/100 1.21 -6.26 -8.28 2D3U 0.68 1 1/100 0.54 -7.11 -9.44 2D3Z 3.86 3 1/88 0.63 -7.60 -9.06 2FDP 0.75 1 1/89 0.68 -14.80 -10.35 2G94 1.75 1 3/5 1.45 -8.64 -12.99 2GBP 0.89 1 1/100 0.87 -5.60 -10.37 2IFB 2.05 2 1/55 1.03 -4.99 -7.41 2IWX 0.87 1 1/100 0.55 -6.76 -9.11 2J77 2.01 1 1/93 1.60 -7.62 -6.67 2J78 0.83 1 2/27 0.73 -6.13 -8.75 2QFU 2.74 4 2/37 0.94 -6.29 -5.70 2QWB 4.35 12 2/15 0.90 -6.64 -3.74 2QWD 2.57 2 1/67 0.91 -7.37 -6.62 2R04 1.99 2 2/8 0.92 -8.84 -8.87 2XIS 1.17 1 1/100 1.14 -6.93 -7.94 2YPI 1.19 1 1/61 0.78 -2.62 -6.57 3PTB 1.31 1 1/100 0.74 -5.06 -6.47 4HMG 1.04 1 1/98 0.85 -6.92 -3.48 7ABP 2.09 1 1/97 1.16 -5.58 -8.78 Average: 1.71 without outliers (rmsd above 4 Å): 1.61 38 first hits 42 first hits Average: 0.87 QASP parameter was modified from 0.01097 to 0.00679 in AutoGrid and AutoDock.

PDB code of the complex RMSD of the first rank result as compared to the X-ray (Å) Energy rank of the lowest RMSD hit Frequency rank/frequency of the best geometry Lowest RMSD (Å) Estimated free energy of binding (kcal/mol) Experimental binding energy (kcal/mol) 1AI5 1.21 1 1/48 0.65 -5.11 -5.08 1AJP 2.56 2 1/47 1.09 -4.40 -3.05 1AMW 1.68 1 1/21 1.59 -5.62 -6.19 1BGQ 1.03 1 1/48 0.71 -6.27 -11.69 1CBR 1.00 1 1/51 0.92 -7.94 -10.58 1D3Q 2.68 2 2/19 1.23 -10.33 -8.88 1D3T 2.29 2 2/20 1.08 -10.08 -8.73 1DWB 9.59 3 1/51 0.53 -6.24 -3.98 1FLR 0.60 1 1/100 0.53 -10.76 -10.98 1GNI 1.56 1 1/49 1.10 -7.73 -11.01 1HVJ 3.12 - -10.03 -14.27 1HVR 0.65 1 1/26 0.54 -14.74 -12.97 1K4G 2.82 4 1/30 1.66 -6.98 -7.99 1KV1 0.64 1 1/98 0.56 -8.91 -8.10 1LIF 2.33 4 1/21 1.08 -5.47 -9.65 1M0N 3.91 - -8.22 -3.03 1M0Q 2.24 5 33/1 1.46 -5.99 -5.30 1OLU 1.34 1 4/10 0.74 -6.96 -6.01 1Q8T 1.88 1 1/77 1.41 -8.29 -6.49 1RBP 0.84 1 1/100 0.56 -9.15 -9.17 1S39 4.29 2 2/11 0.32 -5.29 -10.50 1U33 2.49 1 2/14 1.73 -8.14 -6.28 1ULB 1.88 1 1/100 1.83 -4.66 -7.20 1UWT 2.36 1 1/89 0.87 -6.77 -8.14 1X8R 1.24 1 1/80 0.87 -4.17 -8.36 1XD1 2.92 - -11.12 -10.80 1YDT 2.2 2 1/30 0.74 -10.14 -9.98 1ZC9 2.71 - -4.00 -4.39 2ACK 3.96 8 8/1 1.07 -4.72 -8.97 2BAJ 0.68 1 1/74 0.42 -12.40 -11.46 2BAK 1.28 1 16/2 1.28 -13.78 -10.14 2CEQ 7.14 - -4.66 -9.92 2CET 4.86 - -7.06 -10.94 2CGR 0.87 1 1/43 0.50 -10.68 -9.89 2CPP 1.56 1 1/100 1.21 -6.35 -8.28 2D3U 0.87 1 1/58 0.83 -9.43 -9.44 2D3Z 4.68 3 2/20 0.69 -8.89 -9.06 2FDP 2.35 5 73/1 1.68 -13.67 -10.35 2G94 3.13 - -7.57 -12.99 2GBP 0.99 1 1/90 0.92 -4.18 -10.37 2IFB 2.03 2 1/45 1.10 -6.03 -7.41 2IWX 0.88 1 1/68 0.55 -6.66 -9.11 2J77 1.9 1 1/100 1.85 -7.52 -6.67 2J78 0.83 1 2/11 0.83 -6.41 -8.75 2QFU 2.75 3 3/1 1.02 -6.29 -5.70 2QWB 4.38 13 6/5 1.17 -5.40 -3.74 2QWD 1.36 1 1/54 0.97 -6.80 -6.62 2R04 2.06 2 3/21 1.02 -8.97 -8.87 2XIS 1.20 1 1/95 1.15 -5.43 -7.94 2YPI 4.73 - -3.09 -6.57 3PTB 1.35 1 1/100 0.51 -5.66 -6.47 4HMG 1.82 1 1/22 1.02 -4.78 -3.48 7ABP 2.15 2 2/13 1.64 -4.58 -8.78 Average: 2.34 without outliers (rmsd above 4 Å): 1.83 28 first hits 30 first hits Average: 1.00 The average value of the RMSD between the lowest energy result and experimental structure and the total number of successful first rank predictions (based on lowest energy and highest cluster population, respectively) are indicated at the bottom of the table.

1AI5 Penicillin acylase 2.4 m-nitrophenylacetic acid [ 24 ] 1AJP Penicillin acylase 2.3 2,5-dihydroxyphenylacetic acid [ 24 ] 1AMW Heat shock protein 90 1.9 ADP [ 25 ] 1BGQ Heat shock protein 90 2.5 radicicol [ 26 ] 1CBR Retionic acid binding protein 2.9 retinoic acid [ 27 ] 1D3Q Human thrombin 2.9 benzo [ b ]thiophene derivative [ 28 ] 1D3T Human thrombin 3.0 benzo [ b ]thiophene derivative [ 28 ] 1DWB a-Thrombin 3.2 benzamidine [ 29 ] 1FLR Immunoglobulin 1.9 fluorescein [ 30 ] 1GNI Human serum albumin 2.4 oleic acid [ 31 ] 1HVJ HIV-1 Protease 2.0 A78791 [ 32 ] 1HVR HIV-1 Protease 1.8 XK263 [ 33 ] 1K4G tRNA-guanine transglycosylase 1.7 quinazoline derivative [ 34 ] 1KV1 p38 MAP kinase 2.5 pyrazol derivative [ 35 ] 1LIF Adipocyte lipid-binding protein 1.6 stearic acid [ 36 ] 1M0N Dialkylglycine decarboxylase 2.2 1-aminocyclo-pentanephosphonate [ 37 ] 1M0Q Dialkylglycine decarboxylase 2.0 S-1-amino-ethanephosphonate [ 37 ] 1OLU Branched-chain alpha-ketoacid dehydrogenase kinase 1.9 thiamin diphosphate [ 38 ] 1Q8T cAMP-dependent protein kinase 2.0 (R)-trans-4-(1-aminoethyl)-n-(4-pyridyl) cyclohexanecarboxamide [ 39 ] 1RBP Retinol-binding protein 2.0 retinol [ 40 ] 1S39 tRNA-guanine transglycosylase 2.0 2-aminoquinazolin-4(3H)-one [ 41 ] 1U33 Alpha-amylase 2.0 5-trihydroxy-6-hydroxymethyl-piperidin-2-one [ 42 ] 1ULB Purine nucleoside phosphorylase 2.8 guanine [ 43 ] 1UWT Beta-glycosidase 2.0 D-galactohydroximo-1,5-lactam [ 44 ] 1X8R 3-Phosphoshikimate 1-carboxyvinyltransferase 1.5 phosphonate analogue [ 45 ] 1XD1 Alpha-amylase 2.2 acarbose derived hexasaccharide [ 46 ] 1YDT cAMP-dependent protein kinase 2.3 n-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline [ 47 ] 1ZC9 Dialkylglycine decarboxylase 2.0 pyridoxamine 5-phosphate [ 48 ] 2ACK Acetylcholinesterase 2.4 edrophonium ion [ 49 ] 2BAJ p38alpha Map kinase 2.3 pyrazol derivative [ 50 ] 2BAK p38alpha Map kinase 2.2 nicotinamid derivative [ 50 ] 2CEQ Beta-glycosidase 2.1 glucoimidazole [ 51 ] 2CET Beta-glycosidase 2.0 phenethyl-substituted glucoimidazole [ 51 ] 2CGR Immunoglobulin 2.2 N-trisubstituted guanidine [ 52 ] 2CPP Cytochrome P-450cam 1.6 camphor [ 53 ] 2D3U RNA-dependent RNA polymerase 2.0 non-nucleoside analogue inhibitor I [ 54 ] 2D3Z RNA-dependent RNA polymerase 1.8 non-nucleoside analogue inhibitor II [ 54 ] 2FDP Beta-secretase 2.5 amino-ethylene inhibitor [ 55 ] 2G94 Beta-secretase 1.9 valinamide derivative [ 56 ] 2GBP D-galactose/D-glucose binding protein 1.9 glucose [ 57 ] 2IFB Fatty-acid-binding protein 2.0 palmitic acid [ 58 ] 2IWX Heat shock protein 82 1.5 synthetic macrolactone [ 59 ] 2J77 Beta-glycosidase 2.1 deoxynojirimycin [Gloster, to be published] 2J78 Beta-glycosidase 1.7 gluco-hydroximolactam [Gloster, to be published] 2QFU 3-Phosphoshikimate 1-carboxyvinyltransferase 1.6 shikimate-3-phosphate [ 60 ] 2QWB Neuraminidase 2.0 sialic acid [ 61 ] 2QWD Neuraminidase 2.0 4-amino-Neu5Ac2en [ 61 ] 2R04 Rhinovirus 14 coat protein 3.0 W71, antiviral agent [ 62 ] 2XIS Xylose isomerase 1.6 D-xylitol [ 63 ] 2YPI Triose phosphate isomerase 2.5 2-phosphoglycolic acid [ 64 ] 3PTB b-Trypsin 1.8 benzamidine [ 65 ] 4HMG Hemagglutinin 3.0 sialic acid [ 66 ] 7ABP Arabinose-binding protein 1.7 fucose [ 67 ] Estimation of binding energies Figure 1 shows the correlation between experimentally determined and predicted binding energies as calculated by AutoDock 4.

Publication Year: 2009