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PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations.

(2003) BMC Struct Biol 3

PubMed: 12675950 | PubMedCentral: PMC154089 | DOI: null

The water molecule under the flaps present in all complexes was included in all steps throughout this study except for 1hvr, where the structural water was removed in the preparation of the protease t... be docked with the ligand (the ligand of 1hvr, which is a urea-based inhibitor, does not bind a water molecule in this position).

Publication Year: 2003


Computer-based screening of functional conformers of proteins.

(2008) PLoS Comput Biol 4

PubMed: 18463705 | PubMedCentral: PMC2265533 | DOI: 10.1371/journal.pcbi.1000009

The PDB code of those structures in complex with a substrate analogue are: 1aaq, 1cpi, 1dmp, 1hbv, 1hih, 1hiv, 1hos, 1hps, 1hpv, 1hte, 1htf, 1htg, 1hvi, 1hvj, 1hvk, 1hvl, 1hvr, 1hvs, 1ohr, 1sbg, 2bpv,... 2bpw, 2bpx, 2bpy, 2bpz, 4hvp, 4phv, 5hvp, 7hvp, 8hvp, 9hvp.

For the HIV protease, 73 experimentally determined crystal structures were used: 1a30, 1a8g, 1a9m, 1aaq, 1ajv, 1ajx, 1axa, 1bdr, 1bv7, 1bv9, 1bwa, 1bwb, 1cpi, 1dif, 1dmp, 1gnm, 1gnn, 1gno, 1hbv, 1hih, 1hiv, 1hos, 1hps, 1hpv, 1hpx, 1hsg, 1hte, 1htf, 1htg, 1hvc, 1hvi, 1hvj, 1hvk, 1hvl, 1hvr, 1hvs, 1hwr, 1hxb, 1hxw, 1mer, 1mes, 1met, 1meu, 1mtr, 1odw, 1odx, 1ody, 1ohr, 1pro, 1qbr, 1qbs, 1qbt, 1qbu, 1sbg, 1tcx, 1vij, 1vik, 1ytg, 1yth, 2aid, 2bpv, 2bpw, 2bpx, 2bpy, 2bpz, 2upj, 3aid, 4hvp, 4phv, 5hvp, 7hvp, 8hvp, 9hvp.

Publication Year: 2008


Interaction of HIV-1 aspartic protease with its inhibitor, by molecular dynamics and ab initio fragment molecular orbital method.

(2008) J Synchrotron Radiat 15

PubMed: 18421148 | PubMedCentral: PMC2394819 | DOI: 10.1107/S0909049507068586

Fig. 1 ▶ shows the structure of HIV-1 PR complexed with a cyclic urea inhibitor XK2 [Protein Data Bank (PDB) ID 1hvr ; Lam et al. , 1994 ▶ ] viewed perpendicular to the C 2 axis.

Of the X-ray diffraction structural data deposited in the PDB, two complexes with cyclic urea ( 1hvr and 1ajx ; Hultén et al. , 1997 ▶ ; denoted AH1) and one with a peptide derivative ( 1d4h ; Andersson et al. , 2003 ▶ ; denoted BEH) were selected.

Binding free energy and fragment molecular orbital energy of the complexes with cyclic urea inhibitors [a complex crystal with XK2 (1hvr) and three modelled complexes, XK1, XK3 and XK4] obtained by molecular dynamics and obtained by ABINIT-MP are shown in Table 1 ▶ ( a ).

Publication Year: 2008


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.

i.e. the sum of the absolute value of partial charges was 628.8 in case of Gasteiger charge calculation, while it was 1014.2 using PM6 in case of the protein with PDB entry 4HMG; the sum of absolute values of partial charges was 354.1 with Gasteiger charge calculation and it increased to 570.8 with PM6 partial charge calculation in case of the protein with PDB code 1HVR .

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


A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction.

(2010) BMC Bioinformatics 11

PubMed: 20398404 | PubMedCentral: PMC2868011 | DOI: 10.1186/1471-2105-11-193

Table 1 PDB codes of the protein-ligand complexes in the three test sets HIV protease complexes ( N = 112) 1GNM , 1GNN , 1GNO , 1A30 , 1A9M , 1AAQ , 1AJV , 1AJX , 1B6J , 1B6K , 1B6L , 1B6M , 1BDQ , 1B... 7 , 1BV9 , 1BWA , 1BWB , 1C70 , 1D4K , 1D4L , 1D4Y , 1DIF , 1DMP , 1G2K , 1G35 , 1HBV , 1HEG , 1HIH , 1HII , 1HOS , 1HPO , 1HPS , 1HPV , 1HPX , 1HSH , 1HVH , 1HVI , 1HVJ , 1HVK , 1HVL , 1HVR , 1HVS , 1HWR , 1HXB , 1HXW , 1IIQ , 1IZH , 1IZI , 1LZQ , 1MES , 1MET , 1MEU , 1MRW , 1MRX , 1MSM , 1MSN , 1MTR , 1NH0 , 1ODY , 1OHR , 1PRO , 1QBR , 1QBS , 1QBT , 1QBU , 1SBG , 1SDT , 1SDU , 1SDV , 1SGU , 1SH9 , 1T7J , 1W5V , 1W5W , 1W5X , 1W5Y , 1Z1H , 1Z1R , 1ZP8 , 1ZPA , 1ZSF , 1ZSR , 2AOC , 2AOD , 2AOE , 2AQU , 2AVM , 2AVO , 2AVQ , 2AVS , 2AVV , 2BPV , 2BPY , 2BQV , 2F80 , 2F81 , 2F8G , 2FGU , 2FGV , 2HB3 , 2I0A , 2I0D , 7HVP , 7UPJ , 2HS2 , 2AOG , 2HS1 , 1A94 , 1AID , 1KZK , 1TCX , 3AID Trypsin complexes ( N = 73) 1C1R , 1C5P , 1C5Q , 1C5S , 1C5T , 1CE5 , 1F0T , 1F0U , 1K1I , 1K1J , 1K1L , 1K1M , 1K1N , 1OSS , 1PPC , 1PPH , 1QB1 , 1QB6 , 1QB9 , 1QBN , 1QBO , 1TNG , 1TNH , 1TNI , 1TNJ , 1TNK , 1TNL , 1V2J , 1V2K , 1V2L , 1V2N , 1V2Q , 1V2R , 1V2S , 1V2T , 1V2U , 1V2W , 2A31 , 2BZA , 2FX6 , 1BRA , 1G3B , 1G3C , 1G3D , 1G3E , 1GHZ , 1GI1 , 1GI4 , 1GI6 , 1GJ6 , 1J16 , 1J17 , 1O2H , 1O2J , 1O2K , 1O2N , 1O2O , 1O2Q , 1O2S , 1O2W , 1O2X , 1O2Z , 1O30 , 1O33 , 1O36 , 1O38 , 1O3D , 1O3F , 1O3H , 1O3I , 1O3J , 1O3K , 1V2O Carbonic anhydrase complexes ( N = 44) 1BN1 , 1BN3 , 1BN4 , 1BNN , 1BNQ , 1BNT , 1BNU , 1BNV , 1BNW , 1A42 , 1AVN , 1BCD , 1CIL , 1CIM , 1CIN , 1CNW , 1CNX , 1CNY , 1G1D , 1G45 , 1G46 , 1G48 , 1G4J , 1G4O , 1G52 , 1G53 , 1G54 , 1I9L , 1I9M , 1I9N , 1I9O , 1I9P , 1I9Q , 1IF7 , 1IF8 , 1OKL , 1TTM , 1XPZ , 1XQ0 , 1YDA , 1YDB , 1YDD , 2EZ7 , 2H4N In addition, a set of putative binding poses were prepared for the ligand molecule in each complex in all three test sets.

Publication Year: 2010


Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket.

(2011) PLoS One 6

PubMed: 21559397 | PubMedCentral: PMC3084818 | DOI: 10.1371/journal.pone.0019268

Methods MD simulations The structures for the inhibitor bound complexes were retrieved from Protein Data Bank with PDB codes: 1AJX [32] for AHA001 bound complex, 1HVR [33�... d; for XK263 bound complex and 1HXW [34] for ABT538 bound complex.

Publication Year: 2011


KINARI-Web: a server for protein rigidity analysis.

(2011) Nucleic Acids Res 39

PubMed: 21693559 | PubMedCentral: PMC3125808 | DOI: 10.1093/nar/gkr482

To demonstrate this feature, rigidity analysis of HIV-1 Protease PDB structure 1HVR was performed with and without an inhibitor.

For example, PDB file 1HVR, one of the available X-ray crystallography data files of HIV-1 Protease, contains two chains, A and B, as well as a ligand, XK2.

Publication Year: 2011


Interaction of ganoderic acid on HIV related target: molecular docking studies.

(2011) Bioinformation 7

PubMed: 22347784 | PubMedCentral: PMC3280442 | DOI: null

Hydrogen bonds in 1HVR-Model34 complex were formed through ILE50, ILE50', ASP29 and ASP30 residues.

Interestingly similar hydrogen bonding patterns were also observed in the 1HVR native ligand (XK2) complex in the 1HVR crystal structure.

Publication Year: 2011


Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation.

(2012) Pharmaceuticals (Basel) 5

PubMed: 24281257 | PubMedCentral: PMC3816655 | DOI: 10.3390/ph5101064

PDB ID Protein 1abe L-ARABINOSE-BINDING PROTEIN 1abf L-ARABINOSE-BINDING PROTEIN 1apu ACID PROTEINASE (PENICILLOPEPSIN) 1dbb FAB' FRAGMENT 1dbj FAB' FRAGMENT 1dog GLUCOAMYLASE 1dwb THROMBIN 1epo ENDOT... IA ASPARTIC PROTEINASE 1etr THROMBIN 1ets THROMBIN 1ett THROMBIN 1hpv HIV-1 PROTEASE 1hsl HISTIDINE-BINDING PROTEIN 1htf HIV-1 PROTEASE 1hvr HIV-1 PROTEASE 1nsd NEURAMINIDASE 1pgp 6-PHOSPHOGLUCONATE DEHYDROGENASE 1phg CYTOCHROME P450 1ppc TRYPSIN 1pph TRYPSIN 1rbp RETINOL-BINDING PROTEIN 1tng TRYPSIN 1tnh TRYPSIN 1ulb PURINE NUCLEOSIDE PHOSPHORYLASE 2cgr IGG2B (KAPPA) FAB FRAGMENT 2gbp D-GALACTOSE/D-GLUCOSE-BINDING PROTEIN 2ifb INTESTINAL FATTY ACID BINDING 2phh P-HYDROXYBENZOATE HYDROXYLASE 2r04 RHINOVIRUS 14 (HRV14) 2tsc THYMIDYLATE SYNTHASE 2ypi TRIOSE PHOSPHATE ISOMERASE 3ptb TRYPSIN 4dfr DIHYDROFOLATE REDUCTASE 5abp L-ARABINOSE-BINDING PROTEIN The structural ensembles generated from the PDB structure given by MD in explicit water were prepared as follows.

Publication Year: 2012


Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.

(2009) Acta Pharmacol Sin 30

PubMed: 19935678 | PubMedCentral: PMC4007494 | DOI: 10.1038/aps.2009.159

Target PDB entries a Number of Actives b ACE 1UZF, 1O86, 1UZE * 14 AChE 1ACJ, 1ACL, 1AMN, 1AX9, 1DX6, 1E3Q, 1E66, 1EVE, 1GPK, 1GPN, 1GQR, 1GQS, 1H22, 1H23, 1HBJ, 1JJB, 1OCE, 1ODC, 1U65, 1UT6, ... VOT, 1W4L, 1W6R, 1W76, 1ZGC, 2ACE, 2ACK * , 2BAG, 2C4H, 2C5F, 2C5G, 2C58, 2CEK, 2CKM, 2CMF, 2J3Q, 2VB4 22 AR 1E3G * , 1GS4, 1T5Z, 1T63, 1T65, 1XJ7, 1XOW, 1XQ3, 1Z95, 2AM9, 2AMA, 2AMB, 2AO6, 2AX6, 2AX7, 2AX8, 2AX9, 2AXA, 2HVC, 2OZ7, 2PIO, 2PIP, 2PIQ, 2PIR, 2PIT, 2PIU, 2PIV, 2PIW, 2PIX, 2PKL, 2PNU, 2Q7I, 2Q7J, 2Q7K, 2Q7L, 2Z4J 16 DacA 1CEF, 1CEG * , 1HVB, 1IKG, 1IKI, 1MPL, 1PW1, 1PW8, 1PWC, 1PWD, 1PWG, 1SCW, 1SDE, 1YQS 3 DHFR 1BOZ * , 1KMS, 1KMV, 1S3U, 1S3V, 1S3W, 2DHF, 1DLS, 1U72, 1MVS, 1MVT, 1DLR, 1U71, 1HFP, 1HFQ, 1HFR, 1OHJ, 1OHK, 1DHF, 1DRF, 1PD8, 1PD9 8 ERα 1A52, 1AKF, 1ERE, 1ERR, 1G50, 1GWQ, 1GWR, 1L2I, 1PCG * , 1QKT, 1R5K, 1UOM, 1X7E, 1X7R, 1XP1, 1XP6, 1XP9, 1XPC, 1YIM, 1ZKY, 2AYR, 2B1V, 2B1Z, 2BJ4, 2FAI, 2G44, 2G5O, 2I0J, 2IOG, 2JF9, 2JFA, 2OUZ, 2P15, 2POG, 2Q6J, 2Q70, 2QE4, 3ERD, 3ERT 32 HIV-pr 1AID, 1HVH, 1HVR, 1HWR, 1IZH, 1IZI, 1JLD, 1KZK, 1NPV, 1NPW, 1T3R, 1T7K, 1TCX, 1XL2, 1XL5, 1YT9, 2A4F * , 2AID, 2F3K, 2FDD, 2FDE, 2FGU, 2FGV, 2HC0, 2NXD, 2NXM, 2P3A, 2P3B, 2P3C, 2P3D, 3AID, 4PHV 9 TK 1E2I, 1E2J, 1E2K * , 1E2L, 1E2M, 1E2N, 1E2P, 1KI2, 1KI3, 1KI4, 1KI6, 1KI7, 1KI8, 1KIM, 1OF1, 1P7C, 1QHI, 1VTK, 2KI5, 2VTK, 3VTK 8 a All the X-ray crystal structures of the complexes of each target in complex with ligands were used in the construction of pharmacophore models.

Publication Year: 2009


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4170817

56 , 63 − 65 Table 1 RMSDs of Docking Poses Generated by CHARMMing’s Fragment-Based Docking Protocol and Glide SP and success Rates (defined by the percentage of the ligands whose repo... ted RMSD is below 2.0 Å) a PDB ID resolution (Å) best RMSD (Å) Glide SP RMSD (Å) 1A4Q 1.90 2.61 3.30 1A6W 2.00 1.01 6.72 1AOE 1.60 3.13 1.80 1AQW 1.80 1.88 0.96 1ATL 1.80 1.68 1.09 1BMA 1.80 2.76 1.55 1D3H 1.80 0.99 0.81 1FCZ 1.38 1.06 0.31 1GLQ 1.80 4.71 1.01 1HFC 1.50 2.63 2.36 1HVR 1.80 3.84 0.75 1JAP 1.82 1.41 0.92 1KE5 2.20 1.07 1.75 1MLD 1.83 1.29 1.07 1MMQ 1.90 0.50 0.30 1MTS 1.90 1.96 0.54 1MVC 1.90 0.29 0.94 1NHZ 2.30 0.78 1.89 1NQ7 1.50 0.94 1.26 1QBR 1.80 9.31 0.98 1SRJ 1.80 1.33 0.51 1TXI 1.90 1.66 1.64 3ERT 1.90 0.71 1.59 4DFR 1.70 1.66 10.48 Success Rate: 71% 84% a “Best RMSD” refers to the pose closest to the crystal structure.

Publication Year: 2014