-
1
-
-
0004294950
-
-
Retroviruses. J. C. Cooffin, S. H. Hughes, and H. E. Varmus, editors. Cold Spring Harbor Press, Plainview, NY
-
Brown, P. O. 1997. Integration. In Retroviruses. J. C. Cooffin, S. H. Hughes, and H. E. Varmus, editors. Cold Spring Harbor Press, Plainview, NY.
-
(1997)
Integration
-
-
Brown, P.O.1
-
2
-
-
0032601402
-
HIV integrase structure and function
-
Esposito, D., and R. Craigie. 1999. HIV integrase structure and function. Adv. Virus Res. 52:319-333.
-
(1999)
Adv. Virus Res
, vol.52
, pp. 319-333
-
-
Esposito, D.1
Craigie, R.2
-
3
-
-
0032601403
-
HIV-1 integrase: Structural organization, conformational changes, and catalysis
-
Asante-Appiah, E., and A. M. Skalka. 1999. HIV-1 integrase: structural organization, conformational changes, and catalysis. Adv. Virus Res. 52:351-369.
-
(1999)
Adv. Virus Res
, vol.52
, pp. 351-369
-
-
Asante-Appiah, E.1
Skalka, A.M.2
-
4
-
-
2942553781
-
Structure and function of HIV-1 integrase
-
Chiu, T. K., and D. R. Davies. 2004. Structure and function of HIV-1 integrase. Curr. Top. Med. Chem. 4:965-977.
-
(2004)
Curr. Top. Med. Chem
, vol.4
, pp. 965-977
-
-
Chiu, T.K.1
Davies, D.R.2
-
5
-
-
2942527726
-
HIV-1 integrase: A target for new AIDS chemotherapeutics
-
Anthony, N. J. 2004. HIV-1 integrase: a target for new AIDS chemotherapeutics. Curr. Top. Med. Chem. 4:979-990.
-
(2004)
Curr. Top. Med. Chem
, vol.4
, pp. 979-990
-
-
Anthony, N.J.1
-
6
-
-
13044295993
-
Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design
-
Goldgur, Y., R. Craigie, G. H. Cohen, T. Fujiwara, T. Yoshinaga, T. Fujishita, H. Sugimoto, T. Endo, H. Murai, and D. R. Davies. 1999. Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. Proc. Natl. Acad. Sci. USA. 96:13040-13043.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 13040-13043
-
-
Goldgur, Y.1
Craigie, R.2
Cohen, G.H.3
Fujiwara, T.4
Yoshinaga, T.5
Fujishita, T.6
Sugimoto, H.7
Endo, T.8
Murai, H.9
Davies, D.R.10
-
7
-
-
3042843657
-
HIV-1 integrase inhibitors: A decade of research and two drugs in clinical trial
-
Johnson, A. A., C. Marchand, and Y. Pommier. 2004. HIV-1 integrase inhibitors: a decade of research and two drugs in clinical trial. Curr. Top. Med. Chem. 4:1059-1077.
-
(2004)
Curr. Top. Med. Chem
, vol.4
, pp. 1059-1077
-
-
Johnson, A.A.1
Marchand, C.2
Pommier, Y.3
-
9
-
-
0036836947
-
5-Substituted-1H-tetrazoles as carboxylic acid isosteres: Medicinal chemistry and synthetic methods
-
Herr, R. J. 2002. 5-Substituted-1H-tetrazoles as carboxylic acid isosteres: medicinal chemistry and synthetic methods. Bioorg. Med. Chem. 10:3379-3393.
-
(2002)
Bioorg. Med. Chem
, vol.10
, pp. 3379-3393
-
-
Herr, R.J.1
-
10
-
-
0035855917
-
Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: A molecular dynamics study
-
Ni, H., C. A. Sotriffer, and J. A. McCammon. 2001. Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. J. Med. Chem. 44:3043-3047.
-
(2001)
J. Med. Chem
, vol.44
, pp. 3043-3047
-
-
Ni, H.1
Sotriffer, C.A.2
McCammon, J.A.3
-
11
-
-
0034955827
-
HIV-1 integrase catalytic core: Molecular dynamics and simulated fluorescence decays
-
Laboulais, C., E. Deprez, H. Leh, J. F. Mouscadet, J. C. Brochon, and M. Le Bret. 2001. HIV-1 integrase catalytic core: molecular dynamics and simulated fluorescence decays. Biophys. J. 81:473-489.
-
(2001)
Biophys. J
, vol.81
, pp. 473-489
-
-
Laboulais, C.1
Deprez, E.2
Leh, H.3
Mouscadet, J.F.4
Brochon, J.C.5
Le Bret, M.6
-
12
-
-
0034725381
-
HIV-1 integrase inhibitor interactions at the active site: Prediction of binding modes unaffected by crystal packing
-
Sotriffer, C. A., H. H. Ni, and J. A. McCammon. 2000. HIV-1 integrase inhibitor interactions at the active site: prediction of binding modes unaffected by crystal packing. J. Am. Chem. Soc. 122:6136-6137.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 6136-6137
-
-
Sotriffer, C.A.1
Ni, H.H.2
McCammon, J.A.3
-
13
-
-
1542377504
-
Quantum mechanical/molecular mechanical (QM/MM) docking: An evaluation for known test systems
-
Beierlein, F., H. Lanig, G. Schurer, A. H. C. Horn, and T. Clark. 2003. Quantum mechanical/molecular mechanical (QM/MM) docking: an evaluation for known test systems. Mol. Phys. 101:2469-2480.
-
(2003)
Mol. Phys
, vol.101
, pp. 2469-2480
-
-
Beierlein, F.1
Lanig, H.2
Schurer, G.3
Horn, A.H.C.4
Clark, T.5
-
14
-
-
1842607357
-
Discovery of a novel binding trench in HIV integrase
-
Schames, J. R., R. H. Henchman, J. S. Siegel, C. A. Sotriffer, H. H. Ni, and J. A. McCammon. 2004. Discovery of a novel binding trench in HIV integrase. J. Med. Chem. 47:1879-1881.
-
(2004)
J. Med. Chem
, vol.47
, pp. 1879-1881
-
-
Schames, J.R.1
Henchman, R.H.2
Siegel, J.S.3
Sotriffer, C.A.4
Ni, H.H.5
McCammon, J.A.6
-
15
-
-
29144509688
-
Diketo acid pharmacophore 2. Discovery of structurally diverse inhibitors of HIV-1 integrase
-
Dayam, R., T. Sanchez, and N. Neamati. 2005. Diketo acid pharmacophore 2. Discovery of structurally diverse inhibitors of HIV-1 integrase. J. Med. Chem. 48:8009-8015.
-
(2005)
J. Med. Chem
, vol.48
, pp. 8009-8015
-
-
Dayam, R.1
Sanchez, T.2
Neamati, N.3
-
16
-
-
27444447888
-
Pharmacophore-based design of HIV-1 integrase strand-transfer inhibitors
-
Barreca, M. L., S. Ferro, A. Rao, L. De Luca, M. Zappala, A. M. Monforte, Z. Debyser, M. Witvrouw, and A. Chimirri. 2005. Pharmacophore-based design of HIV-1 integrase strand-transfer inhibitors. J. Med. Chem. 48:7084-7088.
-
(2005)
J. Med. Chem
, vol.48
, pp. 7084-7088
-
-
Barreca, M.L.1
Ferro, S.2
Rao, A.3
De Luca, L.4
Zappala, M.5
Monforte, A.M.6
Debyser, Z.7
Witvrouw, M.8
Chimirri, A.9
-
17
-
-
12144254795
-
b-Diketo acid pharmacophore hypothesis. 1. Discovery of a novel class of HIV-1 integrase inhibitors
-
Dayam, R., T. Sanchez, O. Clement, R. Shoemaker, S. Sei, and N. Neamati. 2005. b-Diketo acid pharmacophore hypothesis. 1. Discovery of a novel class of HIV-1 integrase inhibitors. J. Med. Chem. 48:111-120.
-
(2005)
J. Med. Chem
, vol.48
, pp. 111-120
-
-
Dayam, R.1
Sanchez, T.2
Clement, O.3
Shoemaker, R.4
Sei, S.5
Neamati, N.6
-
18
-
-
14944359976
-
Dynamic receptor-based pharmacophore model development and its application in designing novel HIT-1 integrase inhibitors
-
Deng, J., K. W. Lee, T. Sanchez, M. Cui, N. Neamati, and J. M. Briggs. 2005. Dynamic receptor-based pharmacophore model development and its application in designing novel HIT-1 integrase inhibitors. J. Med. Chem. 48:1496-1505.
-
(2005)
J. Med. Chem
, vol.48
, pp. 1496-1505
-
-
Deng, J.1
Lee, K.W.2
Sanchez, T.3
Cui, M.4
Neamati, N.5
Briggs, J.M.6
-
19
-
-
31544474642
-
HIV integrase inhibitors with nucleobase scaffolds: Discovery of a highly potent anti-HIV agent
-
Nair, V., G. Chi, R. Ptak, and N. Neamati. 2006. HIV integrase inhibitors with nucleobase scaffolds: discovery of a highly potent anti-HIV agent. J. Med. Chem. 49:445-447.
-
(2006)
J. Med. Chem
, vol.49
, pp. 445-447
-
-
Nair, V.1
Chi, G.2
Ptak, R.3
Neamati, N.4
-
20
-
-
33644867878
-
Dynamic pharmacophore model optimization: Identification of novel HIV-1 integrase inhibitors
-
Deng, J., T. Sanchez, N. Neamati, and J. M. Briggs. 2006. Dynamic pharmacophore model optimization: identification of novel HIV-1 integrase inhibitors. J. Med. Chem. 49:1684-1692.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1684-1692
-
-
Deng, J.1
Sanchez, T.2
Neamati, N.3
Briggs, J.M.4
-
21
-
-
33745656139
-
Binding mode prediction of strand transfer HIV-1 integrase inhibitors using Tn5 transposase as a plausible surrogate model for HIV-1 integrase
-
Barreca, M. L., L. De Luca, N. Iraci, and A. Chimirri. 2006. Binding mode prediction of strand transfer HIV-1 integrase inhibitors using Tn5 transposase as a plausible surrogate model for HIV-1 integrase. J. Med. Chem. 49:3994-3997.
-
(2006)
J. Med. Chem
, vol.49
, pp. 3994-3997
-
-
Barreca, M.L.1
De Luca, L.2
Iraci, N.3
Chimirri, A.4
-
22
-
-
33645405333
-
Novel bifunctional quinolonyl diketo acid derivatives as HIV-1 integrase inhibitors: Design, synthesis, biological activities and mechanism of action
-
Di Santo, R., R. Costi, A. Roux, M. Artico, A. Lavecchia, L. Marinelli, E. Novellino, L. Palmisano, M. Andreotti, R. Amici, C. M. Galluzzo, L. Nencioni, A. T. Palamara, Y. Pommier, and M. Marchand. 2006. Novel bifunctional quinolonyl diketo acid derivatives as HIV-1 integrase inhibitors: design, synthesis, biological activities and mechanism of action. J. Med. Chem. 49:1939-1945.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1939-1945
-
-
Di Santo, R.1
Costi, R.2
Roux, A.3
Artico, M.4
Lavecchia, A.5
Marinelli, L.6
Novellino, E.7
Palmisano, L.8
Andreotti, M.9
Amici, R.10
Galluzzo, C.M.11
Nencioni, L.12
Palamara, A.T.13
Pommier, Y.14
Marchand, M.15
-
23
-
-
21644461226
-
Diketoacid HIV-1 integrase inhibitors: An ab initio study
-
Huang, M., W. G. Richards, and G. H. Grant. 2005. Diketoacid HIV-1 integrase inhibitors: an ab initio study. J. Phys. Chem. A. 109:5198-5202.
-
(2005)
J. Phys. Chem. A
, vol.109
, pp. 5198-5202
-
-
Huang, M.1
Richards, W.G.2
Grant, G.H.3
-
24
-
-
25644450220
-
Molecular dynamics studies of the full-length integrase-DNA complex
-
De Luca, L., G. Vistoli, A. Pedretti, M. L. Barreca, and A. Chimirri. 2005. Molecular dynamics studies of the full-length integrase-DNA complex. Biochem. Biophys. Res. Commun. 336:1010-1016.
-
(2005)
Biochem. Biophys. Res. Commun
, vol.336
, pp. 1010-1016
-
-
De Luca, L.1
Vistoli, G.2
Pedretti, A.3
Barreca, M.L.4
Chimirri, A.5
-
25
-
-
3843108916
-
-
Hazuda, D. J., N. J. Anthony, R. P. Gomez, S. M. Jolly, J. S. Wai, L. Zhuang, T. E. Fisher, M. Embrey, J. P. Guare, M. S. Egbertson, J. P. Vacca, J. R. Huff, P. J. Felock, M. V. Witmer, K. A. Stillmock, R. Danovich, J. Grobler, M. D. Miller, A. S. Espeseth, L. X. Jin, I. W. Chen, J. H. Lin, K. Kassahun, J. D. Ellis, B. K. Wong, W. Xu, P. G. Pearson, W. A. Schleif, R. Cortese, E. Emini, V. Summa, M. K. Holloway, and S. D. Young. 2004. A naphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase. Proc. Natl. Acad. Sci. USA. 101:11233-11238.
-
Hazuda, D. J., N. J. Anthony, R. P. Gomez, S. M. Jolly, J. S. Wai, L. Zhuang, T. E. Fisher, M. Embrey, J. P. Guare, M. S. Egbertson, J. P. Vacca, J. R. Huff, P. J. Felock, M. V. Witmer, K. A. Stillmock, R. Danovich, J. Grobler, M. D. Miller, A. S. Espeseth, L. X. Jin, I. W. Chen, J. H. Lin, K. Kassahun, J. D. Ellis, B. K. Wong, W. Xu, P. G. Pearson, W. A. Schleif, R. Cortese, E. Emini, V. Summa, M. K. Holloway, and S. D. Young. 2004. A naphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase. Proc. Natl. Acad. Sci. USA. 101:11233-11238.
-
-
-
-
26
-
-
0034723439
-
Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells
-
Hazuda, D. J., P. Felock, M. Witmer, A. Wolfe, K. Stillmock, J. A. Grobler, A. Espeseth, L. Gabryelski, W. Schleif, C. Blau, and M. D. Miller. 2000. Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells. Science. 287:646-650.
-
(2000)
Science
, vol.287
, pp. 646-650
-
-
Hazuda, D.J.1
Felock, P.2
Witmer, M.3
Wolfe, A.4
Stillmock, K.5
Grobler, J.A.6
Espeseth, A.7
Gabryelski, L.8
Schleif, W.9
Blau, C.10
Miller, M.D.11
-
27
-
-
0037303182
-
S-1360 Shionogi-GlaxoSmithKline
-
Billich, A. 2003. S-1360 Shionogi-GlaxoSmithKline. Curr. Opin. Investig. Drugs. 4:206-209.
-
(2003)
Curr. Opin. Investig. Drugs
, vol.4
, pp. 206-209
-
-
Billich, A.1
-
28
-
-
10744226580
-
Development of resistance against diketo derivatives of human immunodeficiency virus type 1 by progressive accumulation of integrase mutations
-
Fikkert, V., B. Van Maele, J. Vercammen, A. Hantson, B. Van Remoortel, M. Michiels, C. Gurnari, C. Pannecouque, M. De Maeyer, Y. Engelborghs, E. De Clercq, Z. Debyser, and M. Witvrouw. 2003. Development of resistance against diketo derivatives of human immunodeficiency virus type 1 by progressive accumulation of integrase mutations. J. Virol. 77:11459-11470.
-
(2003)
J. Virol
, vol.77
, pp. 11459-11470
-
-
Fikkert, V.1
Van Maele, B.2
Vercammen, J.3
Hantson, A.4
Van Remoortel, B.5
Michiels, M.6
Gurnari, C.7
Pannecouque, C.8
De Maeyer, M.9
Engelborghs, Y.10
De Clercq, E.11
Debyser, Z.12
Witvrouw, M.13
-
29
-
-
18844369136
-
Comparative molecular dynamics simulations of HIV-1 integrase and T66I/M154I mutant: Binding modes and drug resistance to a diketo acid inhibitor
-
Brigo, A., K. W. Lee, F. Fologolari, G. I. Mustata, and J. M. Briggs. 2005. Comparative molecular dynamics simulations of HIV-1 integrase and T66I/M154I mutant: binding modes and drug resistance to a diketo acid inhibitor. Proteins. 59:723-741.
-
(2005)
Proteins
, vol.59
, pp. 723-741
-
-
Brigo, A.1
Lee, K.W.2
Fologolari, F.3
Mustata, G.I.4
Briggs, J.M.5
-
30
-
-
17844395966
-
Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain
-
Brigo, A., K. W. Lee, G. I. Mustata, and J. M. Briggs. 2005. Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain. Biophys. J. 88:3072-3082.
-
(2005)
Biophys. J
, vol.88
, pp. 3072-3082
-
-
Brigo, A.1
Lee, K.W.2
Mustata, G.I.3
Briggs, J.M.4
-
31
-
-
17844406393
-
Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants
-
Lee, M. C., J. Deng, J. M. Briggs, and Y. Duan. 2005. Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. Biophys. J. 88:3133-3146.
-
(2005)
Biophys. J
, vol.88
, pp. 3133-3146
-
-
Lee, M.C.1
Deng, J.2
Briggs, J.M.3
Duan, Y.4
-
32
-
-
0037339235
-
Molecular dynamics studies of wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: Mechanism for inhibition and drug resistance
-
Barreca, M. L., K. W. Lee, A. Chimirri, and J. M. Briggs. 2003. Molecular dynamics studies of wild-type and double mutant HIV-1 integrase complexed with the 5CITEP inhibitor: mechanism for inhibition and drug resistance. Biophys. J. 84:1450-1463.
-
(2003)
Biophys. J
, vol.84
, pp. 1450-1463
-
-
Barreca, M.L.1
Lee, K.W.2
Chimirri, A.3
Briggs, J.M.4
-
33
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague, S. J. 2003. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discov. 2:527-541.
-
(2003)
Nat. Rev. Drug Discov
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
34
-
-
0037157153
-
Computational drug design accommodating receptor flexibility: The relaxed complex scheme
-
Lin, J. H., A. L. Perryman, J. R. Schames, and J. A. McCammon. 2002. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J. Am. Chem. Soc. 124:5632-5633.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 5632-5633
-
-
Lin, J.H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
35
-
-
0036680063
-
Protein flexibility and drug design: How to hit a moving target
-
Carlson, H. A. 2002. Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 6:447-452.
-
(2002)
Curr. Opin. Chem. Biol
, vol.6
, pp. 447-452
-
-
Carlson, H.A.1
-
36
-
-
0033974667
-
Accommodating protein flexibility in computational drug design
-
Carlson, H. A., and J. A. McCammon. 2000. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 57:213-218.
-
(2000)
Mol. Pharmacol
, vol.57
, pp. 213-218
-
-
Carlson, H.A.1
McCammon, J.A.2
-
37
-
-
0036286654
-
Free energy simulations come of age: Protein-ligand recognition
-
Simonson, T., G. Archontis, and M. Karplus. 2002. Free energy simulations come of age: protein-ligand recognition. Acc. Chem. Res. 35:430-437.
-
(2002)
Acc. Chem. Res
, vol.35
, pp. 430-437
-
-
Simonson, T.1
Archontis, G.2
Karplus, M.3
-
38
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme
-
Warshel, A., and M. Levitt. 1976. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:227-249.
-
(1976)
J. Mol. Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
39
-
-
84986513644
-
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
-
Field, M. J., P. A. Bash, and M. Karplus. 1990. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11:700-733.
-
(1990)
J. Comput. Chem
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
40
-
-
0001491955
-
Hybrid quantum and molecular mechanical simulations: An alternative avenue to solvent effects in organic chemistry
-
Gao, J. 1996. Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29:298-305.
-
(1996)
Acc. Chem. Res
, vol.29
, pp. 298-305
-
-
Gao, J.1
-
41
-
-
0346726109
-
How enzymes work: Analysis by modern rate theory and computer simulations
-
García-Viloca, M., J. Gao, M. Karplus, and D. G. Truhlar. 2004. How enzymes work: analysis by modern rate theory and computer simulations. Science. 303:186-195.
-
(2004)
Science
, vol.303
, pp. 186-195
-
-
García-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
42
-
-
1642410886
-
Theoretical insights in enzyme catalysis
-
Martí, S., M. Roca, J. Andres, V. Moliner, E. Silla, I. Tuñón, and J. Bertrán. 2004. Theoretical insights in enzyme catalysis. Chem. Soc. Rev. 33:98-107.
-
(2004)
Chem. Soc. Rev
, vol.33
, pp. 98-107
-
-
Martí, S.1
Roca, M.2
Andres, J.3
Moliner, V.4
Silla, E.5
Tuñón, I.6
Bertrán, J.7
-
43
-
-
0027125907
-
A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
-
Gao, J., and X. Xia. 1992. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. Science. 258:631-635.
-
(1992)
Science
, vol.258
, pp. 631-635
-
-
Gao, J.1
Xia, X.2
-
44
-
-
0037459224
-
Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase
-
García-Viloca, M., D. G. Truhlar, and J. Gao. 2003. Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase. J. Mol. Biol. 327:549-560.
-
(2003)
J. Mol. Biol
, vol.327
, pp. 549-560
-
-
García-Viloca, M.1
Truhlar, D.G.2
Gao, J.3
-
45
-
-
11144235131
-
A combined QM/MM approach to protein-ligand interactions: Polarization effects of the HIV-1 protease on selected high affinity inhibitors
-
Hensen, C., J. Hermann, K. Nam, S. Ma, J. Gao, and H. D. Höltje. 2004. A combined QM/MM approach to protein-ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors. J. Med. Chem. 47:6673-6680.
-
(2004)
J. Med. Chem
, vol.47
, pp. 6673-6680
-
-
Hensen, C.1
Hermann, J.2
Nam, K.3
Ma, S.4
Gao, J.5
Höltje, H.D.6
-
46
-
-
20344362412
-
Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics
-
Gräter, F., S. M. Schwarzl, A. Dejaegere, S. Fischer, and J. C. Smith. 2005. Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J. Phys. Chem. B. 109:10474-10483.
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 10474-10483
-
-
Gräter, F.1
Schwarzl, S.M.2
Dejaegere, A.3
Fischer, S.4
Smith, J.C.5
-
47
-
-
33846426835
-
A computational study of the protein-ligand interactions in CDK2 inhibitors: Using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity
-
Alzate-Morales, J. H., R. Contreras, A. Soriano, I. Tuñón, and E. Silla. 2007. A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity. Biophys. J. 92:430-439.
-
(2007)
Biophys. J
, vol.92
, pp. 430-439
-
-
Alzate-Morales, J.H.1
Contreras, R.2
Soriano, A.3
Tuñón, I.4
Silla, E.5
-
48
-
-
34748912966
-
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase
-
Alves, C. N., S. Martí, R. Castillo, J. Andrés, V. Moliner, I. Tuñó n, and E. Silla. 2007. A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase. Chem. Eur. J. 13:7715-7724.
-
(2007)
Chem. Eur. J
, vol.13
, pp. 7715-7724
-
-
Alves, C.N.1
Martí, S.2
Castillo, R.3
Andrés, J.4
Moliner, V.5
Tuñó n, I.6
Silla, E.7
-
49
-
-
85031350205
-
-
Hypercube. 2002. HyperChem 7.5. Hypercube, Gainesville, FL.
-
Hypercube. 2002. HyperChem 7.5. Hypercube, Gainesville, FL.
-
-
-
-
50
-
-
0028305457
-
Prediction of pH-dependent properties of proteins
-
Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
-
(1994)
J. Mol. Biol
, vol.238
, pp. 415-436
-
-
Antosiewicz, J.1
McCammon, J.A.2
Gilson, M.K.3
-
51
-
-
0027477251
-
Multiple-site titration and molecular modeling - two rapid methods for computing energies and forces for ionizable groups in proteins
-
Gilson, M. K. 1993. Multiple-site titration and molecular modeling - two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins. 15:266-282.
-
(1993)
Proteins
, vol.15
, pp. 266-282
-
-
Gilson, M.K.1
-
52
-
-
0842341771
-
Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model
-
Dewar, M. J. S., E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart. 1985. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107:3902-3909.
-
(1985)
J. Am. Chem. Soc
, vol.107
, pp. 3902-3909
-
-
Dewar, M.J.S.1
Zoebisch, E.G.2
Healy, E.F.3
Stewart, J.J.P.4
-
53
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118: 11225-11236.
-
(1996)
J. Am. Chem. Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
54
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
56
-
-
0000831054
-
The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials
-
Field, M. J., M. Albe, C. Bret, F. Proust-De Martin, and A. Thomas. 2000. The dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials. J. Comput. Chem. 21:1088-1100.
-
(2000)
J. Comput. Chem
, vol.21
, pp. 1088-1100
-
-
Field, M.J.1
Albe, M.2
Bret, C.3
Proust-De Martin, F.4
Thomas, A.5
-
57
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic behaviour
-
Becke, A. D. 1988. Density-functional exchange-energy approximation with correct asymptotic behaviour. Phys. Rev. A. 38:3098-3100.
-
(1988)
Phys. Rev. A
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
58
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee, C., W. Yang, and R. G. Parr. 1988. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter. 37:785-789.
-
(1988)
Phys. Rev. B Condens. Matter
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
59
-
-
27144445025
-
Antibiotic binding to monozinc CphA beta-lactamase from Aeromonas hydropila: Quantum mechanical/molecular mechanical and density functional theory studies
-
Xu, D., Y. Zhou, D. Xie, and H. Guo. 2005. Antibiotic binding to monozinc CphA beta-lactamase from Aeromonas hydropila: quantum mechanical/molecular mechanical and density functional theory studies. J. Med. Chem. 48:6679-6689.
-
(2005)
J. Med. Chem
, vol.48
, pp. 6679-6689
-
-
Xu, D.1
Zhou, Y.2
Xie, D.3
Guo, H.4
-
60
-
-
33845926809
-
Improving the QM/MM description of chemical processes: A dual level strategy to explore the potential energy surface in very large systems
-
Marti, S., V. Moliner, and I. Tunon. 2005. Improving the QM/MM description of chemical processes: a dual level strategy to explore the potential energy surface in very large systems. J. Chem. Theory Comput. 1:1008-1016.
-
(2005)
J. Chem. Theory Comput
, vol.1
, pp. 1008-1016
-
-
Marti, S.1
Moliner, V.2
Tunon, I.3
-
61
-
-
84986513567
-
Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
-
Breneman, C. M., and K. B. Wiberg. 1990. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 11:361-373.
-
(1990)
J. Comput. Chem
, vol.11
, pp. 361-373
-
-
Breneman, C.M.1
Wiberg, K.B.2
-
62
-
-
0030033588
-
Cation-pi interactions in chemistry and biology: A new view of benzene, Phe, Tyr, and Trp
-
Dougherty, D. A. 1996. Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science. 271:163-168.
-
(1996)
Science
, vol.271
, pp. 163-168
-
-
Dougherty, D.A.1
-
63
-
-
4243468938
-
The cation-π interaction
-
Ma, J. C., and D. A. Dougherty. 1997. The cation-π interaction. Chem. Rev. 97:1303-1324.
-
(1997)
Chem. Rev
, vol.97
, pp. 1303-1324
-
-
Ma, J.C.1
Dougherty, D.A.2
-
64
-
-
0037066730
-
Structural determinants for HIV-1 integrase inhibition by β-diketoacids
-
Marchand, C., X. Zhang, G. C. G. Pais, K. Cowasange, N. Neamati, T. R. Burke Jr., and Y. Pommier. 2002. Structural determinants for HIV-1 integrase inhibition by β-diketoacids. J. Biol. Chem. 277:12596-12603.
-
(2002)
J. Biol. Chem
, vol.277
, pp. 12596-12603
-
-
Marchand, C.1
Zhang, X.2
Pais, G.C.G.3
Cowasange, K.4
Neamati, N.5
Burke Jr., T.R.6
Pommier, Y.7
-
65
-
-
0041353616
-
Metal-dependent inhibition of HIV-1 integrase by beta-diketo acids and resistance of the soluble double-mutant (F185K/C280S)
-
Marchand, C., A. A. Johnson, R. G. Karki, G. C. G. Pais, X. C. Zhang, K. Cowansage, T. A. Patel, M. C. Nicklaus, T. R. Burke, and Y. Pommier. 2003. Metal-dependent inhibition of HIV-1 integrase by beta-diketo acids and resistance of the soluble double-mutant (F185K/C280S). Mol. Pharmacol. 64:600-609.
-
(2003)
Mol. Pharmacol
, vol.64
, pp. 600-609
-
-
Marchand, C.1
Johnson, A.A.2
Karki, R.G.3
Pais, G.C.G.4
Zhang, X.C.5
Cowansage, K.6
Patel, T.A.7
Nicklaus, M.C.8
Burke, T.R.9
Pommier, Y.10
-
66
-
-
0037130159
-
Structure activity of 3-aryl-1,3-diketo-containing compounds as HIV-1 integrase inhibitors
-
Pais, G. C., X. Zhang, C. Marchand, N. Neamati, K. Cowasange, E. S. Svarvskaia, V. K. Pathak, Y. Tang, M. Nicklaus, Y. Pommier, and T. R. Burke Jr. 2002. Structure activity of 3-aryl-1,3-diketo-containing compounds as HIV-1 integrase inhibitors. J. Med. Chem. 45:3184-3194.
-
(2002)
J. Med. Chem
, vol.45
, pp. 3184-3194
-
-
Pais, G.C.1
Zhang, X.2
Marchand, C.3
Neamati, N.4
Cowasange, K.5
Svarvskaia, E.S.6
Pathak, V.K.7
Tang, Y.8
Nicklaus, M.9
Pommier, Y.10
Burke Jr., T.R.11
-
67
-
-
0030828521
-
Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-crosslinking
-
Jenkins, T. M., D. Esposito, A. Engelman, and R. Cragie. 1997. Critical contacts between HIV-1 integrase and viral DNA identified by structure-based analysis and photo-crosslinking. EMBO J. 16:6849-6859.
-
(1997)
EMBO J
, vol.16
, pp. 6849-6859
-
-
Jenkins, T.M.1
Esposito, D.2
Engelman, A.3
Cragie, R.4
-
68
-
-
0032189652
-
Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction
-
Esposito, D., and R. Cragie. 1998. Sequence specificity of viral end DNA binding by HIV-1 integrase reveals critical regions for protein-DNA interaction. EMBO J. 17:5832-5843.
-
(1998)
EMBO J
, vol.17
, pp. 5832-5843
-
-
Esposito, D.1
Cragie, R.2
-
69
-
-
0030875813
-
Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active enzyme-DNA complex by photo-cross-linking
-
Heuer, T. S., and P. O. Brown. 1997. Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active enzyme-DNA complex by photo-cross-linking. Biochemistry. 36:10655-10665.
-
(1997)
Biochemistry
, vol.36
, pp. 10655-10665
-
-
Heuer, T.S.1
Brown, P.O.2
-
70
-
-
0032510707
-
Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex
-
Heuer, T. S., and P. O. Brown. 1998. Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex. Biochemistry. 37:6667-6678.
-
(1998)
Biochemistry
, vol.37
, pp. 6667-6678
-
-
Heuer, T.S.1
Brown, P.O.2
-
71
-
-
34247359998
-
Calculation of binding energy using BLYP/MM for HIV-1 integrase complexed with the S-1360 and two analogues
-
Alves, C. N., S. Martí, R. Castillo, J. Andrés, V. Moliner, I. Tuñón, and E. Silla. 2007. Calculation of binding energy using BLYP/MM for HIV-1 integrase complexed with the S-1360 and two analogues. Bioorg. Med. Chem. 15:3818-3824.
-
(2007)
Bioorg. Med. Chem
, vol.15
, pp. 3818-3824
-
-
Alves, C.N.1
Martí, S.2
Castillo, R.3
Andrés, J.4
Moliner, V.5
Tuñón, I.6
Silla, E.7
-
72
-
-
33646756863
-
A density functional study of flavonoid compounds with anti-HIV activity
-
Lameira, J., C. N. Alves, V. Moliner, and E. Silla. 2006. A density functional study of flavonoid compounds with anti-HIV activity. Eur. J. Med. Chem. 41:616-623.
-
(2006)
Eur. J. Med. Chem
, vol.41
, pp. 616-623
-
-
Lameira, J.1
Alves, C.N.2
Moliner, V.3
Silla, E.4
-
73
-
-
33748750068
-
Structure-activity relationship study of flavone compounds with anti-HIV-1 integrase activity: A density functional theory study
-
Lameira, J., I. G. Medeiros, M. Reis A. S. Santos, and C. N. Alves. 2006. Structure-activity relationship study of flavone compounds with anti-HIV-1 integrase activity: a density functional theory study. Bioorg. Med. Chem. 14:7105-7112.
-
(2006)
Bioorg. Med. Chem
, vol.14
, pp. 7105-7112
-
-
Lameira, J.1
Medeiros, I.G.2
Reis, M.3
Santos, A.S.4
Alves, C.N.5
-
74
-
-
85031368490
-
-
Dennington II, R, T. Keith, J. Millam, K. Eppinnett, H. W. Lee, and R. Gilliland. 2003. GaussView Version 3.09. Semichem, Shawnee Mission, KS
-
Dennington II, R., T. Keith, J. Millam, K. Eppinnett, H. W. Lee, and R. Gilliland. 2003. GaussView Version 3.09. Semichem, Shawnee Mission, KS.
-
-
-
-
75
-
-
0034727864
-
4-aryl-2,4-dioxobutanoic acid inhibitors of HIV-1 integrase and viral replication in cells
-
Wai, J. S., M. S. Egbertson, L. S. Payne, T. E. Fisher, M. W. Embrey, L. O. Tran, J. Y. Melamed, H. M. Langford, J. P. Guare, L. G. Zhuang, V. E. Grey, J. P. Vacca, M. K. Holloway, A. M. Naylor-Olsen, D. J. Hazuda, P. J. Felock, A. L. Wolfe, K. A. Stillmock, W. A. Schleif, L. J. Gabryelski, and S. D. Young. 2000. 4-aryl-2,4-dioxobutanoic acid inhibitors of HIV-1 integrase and viral replication in cells. J. Med. Chem. 43:4923-4926.
-
(2000)
J. Med. Chem
, vol.43
, pp. 4923-4926
-
-
Wai, J.S.1
Egbertson, M.S.2
Payne, L.S.3
Fisher, T.E.4
Embrey, M.W.5
Tran, L.O.6
Melamed, J.Y.7
Langford, H.M.8
Guare, J.P.9
Zhuang, L.G.10
Grey, V.E.11
Vacca, J.P.12
Holloway, M.K.13
Naylor-Olsen, A.M.14
Hazuda, D.J.15
Felock, P.J.16
Wolfe, A.L.17
Stillmock, K.A.18
Schleif, W.A.19
Gabryelski, L.J.20
Young, S.D.21
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