-
1
-
-
0031027901
-
Molecular basis of HIV-1 protease drug resistance: Structural analysis of mutant proteases complexed with cyclic urea inhibitors
-
Ala, P.J., Huston, E.E., Klabe, R.M., McCabe, D.D., Duke, J.L., Rizzo, C.J., Korant, B.D., DeLoskey, R.J., Lam, P.Y.S., Hodge, C.N., et al. 1997. Molecular basis of HIV-1 protease drug resistance: Structural analysis of mutant proteases complexed with cyclic urea inhibitors. Biochemistry 36: 1573-1580.
-
(1997)
Biochemistry
, vol.36
, pp. 1573-1580
-
-
Ala, P.J.1
Huston, E.E.2
Klabe, R.M.3
McCabe, D.D.4
Duke, J.L.5
Rizzo, C.J.6
Korant, B.D.7
DeLoskey, R.J.8
Lam, P.Y.S.9
Hodge, C.N.10
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola, A., and Haak, J.R. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
3
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
4
-
-
0004195760
-
-
University of California, San Francisco
-
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Wang J., Ross, W.S., Simmerling, C., Darden, T., Merz, K.M., Stanton, R.V., et al. 2002. AMBER 7. University of California, San Francisco.
-
(2002)
AMBER 7
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Wang, J.5
Ross, W.S.6
Simmerling, C.7
Darden, T.8
Merz, K.M.9
Stanton, R.V.10
-
5
-
-
0028958868
-
Flap opening in HIV-1 protease simulated by "activated" molecular dynamics
-
Collins, J.R., Burt, S.K., and Erickson, J.W. 1995. Flap opening in HIV-1 protease simulated by "activated" molecular dynamics. Nat. Struct. Biol. 2: 334-338.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 334-338
-
-
Collins, J.R.1
Burt, S.K.2
Erickson, J.W.3
-
6
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M.L., and Darden, T. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
-
7
-
-
0036147844
-
Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations
-
Freedberg, D.I., Ishima, R., Jacob, J., Wang, Y.-X., Kustanovich, I., Louis, J.M., and Torchia, D.A. 2002. Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci. 11: 221-232.
-
(2002)
Protein Sci.
, vol.11
, pp. 221-232
-
-
Freedberg, D.I.1
Ishima, R.2
Jacob, J.3
Wang, Y.-X.4
Kustanovich, I.5
Louis, J.M.6
Torchia, D.A.7
-
8
-
-
0001326141
-
Rational design of HIV protease inhibitors
-
(eds. W. Chiu et al.). Oxford University Press, Oxford, UK
-
Hodge, C.N., Straatsma, T.P., and McCammon, J.A. 1997. Rational design of HIV protease inhibitors. In Structural biology of viruses (eds. W. Chiu et al.), pp. 451-473. Oxford University Press, Oxford, UK.
-
(1997)
Structural Biology of Viruses
, pp. 451-473
-
-
Hodge, C.N.1
Straatsma, T.P.2
McCammon, J.A.3
-
9
-
-
0030442990
-
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
-
Hooft, R.W., Sander, C., and Vriend, G. 1996. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins Struct. Funct. Genet. 26: 363-376.
-
(1996)
Proteins Struct. Funct. Genet.
, vol.26
, pp. 363-376
-
-
Hooft, R.W.1
Sander, C.2
Vriend, G.3
-
10
-
-
0033200247
-
Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function
-
Ishima, R., Freedberg, D.I., Wang, Y.-X., Louis, J.M., and Torchia, D.A. 1999. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Struct. Fold. Des. 7: 1047-1055.
-
(1999)
Struct. Fold. Des.
, vol.7
, pp. 1047-1055
-
-
Ishima, R.1
Freedberg, D.I.2
Wang, Y.-X.3
Louis, J.M.4
Torchia, D.A.5
-
11
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., and Madura, J.D. 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
-
12
-
-
0037634016
-
A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex
-
Katoh, E., Louis, J.M., Yamazaki, T., Gronenborn, A.M., Torchia, D.A., and Ishima, R. 2003. A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex. Protein Sci. 12: 1376-1385.
-
(2003)
Protein Sci.
, vol.12
, pp. 1376-1385
-
-
Katoh, E.1
Louis, J.M.2
Yamazaki, T.3
Gronenborn, A.M.4
Torchia, D.A.5
Ishima, R.6
-
13
-
-
0032537482
-
Resistance to HIV protease inhibitors: A comparison of enzyme inhibition and antiviral potency
-
Klabe, R.M., Bacheler, L.T., Ala, P.J., Erickson-Viitanen, S., and Meek, J.L. 1998. Resistance to HIV protease inhibitors: A comparison of enzyme inhibition and antiviral potency. Biochemistry 37: 8735-8742.
-
(1998)
Biochemistry
, vol.37
, pp. 8735-8742
-
-
Klabe, R.M.1
Bacheler, L.T.2
Ala, P.J.3
Erickson-Viitanen, S.4
Meek, J.L.5
-
14
-
-
0037963159
-
Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations
-
Kurt, N., Scott, W.R.P., Schiffer, C.A., and Haliloglu, T. 2003. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: A structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins Struct. Funct. Genet. 51: 409-422.
-
(2003)
Proteins Struct. Funct. Genet.
, vol.51
, pp. 409-422
-
-
Kurt, N.1
Scott, W.R.P.2
Schiffer, C.A.3
Haliloglu, T.4
-
15
-
-
0037157153
-
Computational drug design accommodating receptor flexibility: The Relaxed Complex scheme
-
Lin, J.-H., Perryman, A.L., Schames, J.R., and McCammon, J.A. 2002. Computational drug design accommodating receptor flexibility: The Relaxed Complex scheme. JACS 124: 5632-5633.
-
(2002)
JACS
, vol.124
, pp. 5632-5633
-
-
Lin, J.-H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
16
-
-
0037231646
-
The Relaxed Complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
-
-. 2003. The Relaxed Complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers 68: 47-62.
-
(2003)
Biopolymers
, vol.68
, pp. 47-62
-
-
-
17
-
-
0037043652
-
Antiretroviral-drug resistance among patients recently infected with HIV
-
Little, S.J., Holte, S., Routy, J.P., Daar, E.S., Markowitz, M., Collier, A.C., Koup, R.A., Mellors, J.W., Connick, E., Conway, B., et al. 2002. Antiretroviral-drug resistance among patients recently infected with HIV. N. Engl. J. Med. 347: 385-394.
-
(2002)
N. Engl. J. Med.
, vol.347
, pp. 385-394
-
-
Little, S.J.1
Holte, S.2
Routy, J.P.3
Daar, E.S.4
Markowitz, M.5
Collier, A.C.6
Koup, R.A.7
Mellors, J.W.8
Connick, E.9
Conway, B.10
-
18
-
-
0032574705
-
Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis
-
Luque, I., Todd, M.J., Gomez, J., Semo, N., and Freire, E. 1998. Molecular basis of resistance to HIV-1 protease inhibition: A plausible hypothesis. Biochemistry 37: 5791-5797.
-
(1998)
Biochemistry
, vol.37
, pp. 5791-5797
-
-
Luque, I.1
Todd, M.J.2
Gomez, J.3
Semo, N.4
Freire, E.5
-
19
-
-
0035370444
-
Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes
-
Mahalingam, B., Louis, J.M., Hung, J., Harrison, R.W., and Weber, I.T. 2001. Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes. Proteins Struct. Funct. Genet. 43: 455-464.
-
(2001)
Proteins Struct. Funct. Genet.
, vol.43
, pp. 455-464
-
-
Mahalingam, B.1
Louis, J.M.2
Hung, J.3
Harrison, R.W.4
Weber, I.T.5
-
20
-
-
0036643501
-
Combining mutations in HIV-1 protease to understand mechanisms of resistance
-
Mahalingam, B., Boross, P., Wang, Y.-F., Louis, J.M., Fischer, C.C., Tozser, J., Harrison, R.W., and Weber, I.T. 2002. Combining mutations in HIV-1 protease to understand mechanisms of resistance. Proteins Struct. Funct. Genet. 48: 107-116.
-
(2002)
Proteins Struct. Funct. Genet.
, vol.48
, pp. 107-116
-
-
Mahalingam, B.1
Boross, P.2
Wang, Y.-F.3
Louis, J.M.4
Fischer, C.C.5
Tozser, J.6
Harrison, R.W.7
Weber, I.T.8
-
21
-
-
0030468331
-
Human immunodeficiency virus: Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex
-
Maschera, B., Darby, G., Palu, G., Wright, L.L., Tisdale, M., Myers, R., Blair, E.D., and Fufine, E.S. 1996. Human immunodeficiency virus: Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J. Biol. Chem. 271: 33231-33235.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 33231-33235
-
-
Maschera, B.1
Darby, G.2
Palu, G.3
Wright, L.L.4
Tisdale, M.5
Myers, R.6
Blair, E.D.7
Fufine, E.S.8
-
22
-
-
0032870608
-
Improving macromolecular electrostatics calculations
-
Nielsen, J.E., Andersen, K.V., Honig, B., Hooft, R.W., Klebe, G., Vriend, G., and Wade, R.C. 1999. Improving macromolecular electrostatics calculations. Protein Eng. 12: 657-662.
-
(1999)
Protein Eng.
, vol.12
, pp. 657-662
-
-
Nielsen, J.E.1
Andersen, K.V.2
Honig, B.3
Hooft, R.W.4
Klebe, G.5
Vriend, G.6
Wade, R.C.7
-
23
-
-
0036078615
-
Overcoming drug resistance in HIV-1 chemotherapy: The binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of HIV-1 protease
-
Ohtaka, H., Velazquez-Campoy, A., Xie, D., and Freire, E. 2002. Overcoming drug resistance in HIV-1 chemotherapy: The binding thermodynamics of Amprenavir and TMC-126 to wild-type and drug-resistant mutants of HIV-1 protease. Protein Sci. 11: 1908-1916.
-
(2002)
Protein Sci.
, vol.11
, pp. 1908-1916
-
-
Ohtaka, H.1
Velazquez-Campoy, A.2
Xie, D.3
Freire, E.4
-
24
-
-
0036306459
-
Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
-
Piana, S., Carloni, P., and Parrinello, M. 2002a. Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J. Mol. Biol. 319: 567-583.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 567-583
-
-
Piana, S.1
Carloni, P.2
Parrinello, M.3
-
25
-
-
0036786493
-
Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations
-
Piana, S., Carloni, P., and Rothlisberger, U. 2002b. Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Sci. 11: 2393-2402.
-
(2002)
Protein Sci.
, vol.11
, pp. 2393-2402
-
-
Piana, S.1
Carloni, P.2
Rothlisberger, U.3
-
26
-
-
0034283345
-
How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease
-
Prabu-Jeyabalan, M., Nalivaika, E., and Schiffer, C.A. 2000. How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J. Mol. Biol. 301: 1207-1220.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 1207-1220
-
-
Prabu-Jeyabalan, M.1
Nalivaika, E.2
Schiffer, C.A.3
-
27
-
-
0037046143
-
Anisotropic dynamics of the JE-2147-HIV protease complex: Drug resistance and thermodynamic binding mode examined in a 1.09 A structure
-
Reiling, K.K., Endres, N.F., Dauber, D.S., Craik, C.S., and Stroud, R.M. 2002. Anisotropic dynamics of the JE-2147-HIV protease complex: Drug resistance and thermodynamic binding mode examined in a 1.09 A structure. Biochemistry 41: 4582-4594.
-
(2002)
Biochemistry
, vol.41
, pp. 4582-4594
-
-
Reiling, K.K.1
Endres, N.F.2
Dauber, D.S.3
Craik, C.S.4
Stroud, R.M.5
-
28
-
-
0037250521
-
Human immunodeficiency virus reverse transcriptase and protease sequence database
-
Rhee, S.-Y., Gonzales, M.J., Kantor, R., Betts, B.J., Ravela, J., and Shafer, R.W. 2003. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res. 31: 298-303.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 298-303
-
-
Rhee, S.-Y.1
Gonzales, M.J.2
Kantor, R.3
Betts, B.J.4
Ravela, J.5
Shafer, R.W.6
-
29
-
-
0032127391
-
Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease
-
Rick, S.W., Erickson, J.W., and Burt, S.K. 1998. Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 protease. Proteins 32: 7-16.
-
(1998)
Proteins
, vol.32
, pp. 7-16
-
-
Rick, S.W.1
Erickson, J.W.2
Burt, S.K.3
-
30
-
-
0032562224
-
Domain flexibility in retroviral proteases: Structural implications for drug resistance mutations
-
Rose, R.B., Craik, C.S., and Stroud, R.M. 1998. Domain flexibility in retroviral proteases: Structural implications for drug resistance mutations. Biochemistry 37: 2607-2621.
-
(1998)
Biochemistry
, vol.37
, pp. 2607-2621
-
-
Rose, R.B.1
Craik, C.S.2
Stroud, R.M.3
-
31
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J.-P., Ciccotti, G., and Berendsen, H.J.C. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
32
-
-
0004223683
-
-
University of California, San Francisco, CA
-
Schafmeister, C.E.A.F., Ross, W.S., and Romanovski, V. 1995. LEaP. University of California, San Francisco, CA.
-
(1995)
LEaP
-
-
Schafmeister, C.E.A.F.1
Ross, W.S.2
Romanovski, V.3
-
33
-
-
0034483901
-
Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
-
Scott, W.R. and Schiffer, C.A. 2000. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Struct. Fold. Des. 8: 1259-1265.
-
(2000)
Struct. Fold. Des.
, vol.8
, pp. 1259-1265
-
-
Scott, W.R.1
Schiffer, C.A.2
-
34
-
-
0026344399
-
The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU
-
Spinelli, S., Liu, Q.Z., Alzari, P.M., Hirel, P.H., and Poljak, R.J. 1991. The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU. Biochemie 73: 1391-1396.
-
(1991)
Biochemie
, vol.73
, pp. 1391-1396
-
-
Spinelli, S.1
Liu, Q.Z.2
Alzari, P.M.3
Hirel, P.H.4
Poljak, R.J.5
-
35
-
-
0029909674
-
Structure-based design of HIV protease inhibitors: Sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors
-
Thaisrivongs, S., Skulnick, H.I., Turner, S.R., Strohback, J.W., Tommasi, R.A., Johnson, P.D., Aristoff, P.A., Judge, T.M., Gammill, R.B., Morris, J.K., et al. 1996. Structure-based design of HIV protease inhibitors: Sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors. J. Med. Chem. 39: 4349-4353.
-
(1996)
J. Med. Chem.
, vol.39
, pp. 4349-4353
-
-
Thaisrivongs, S.1
Skulnick, H.I.2
Turner, S.R.3
Strohback, J.W.4
Tommasi, R.A.5
Johnson, P.D.6
Aristoff, P.A.7
Judge, T.M.8
Gammill, R.B.9
Morris, J.K.10
-
36
-
-
0035910029
-
Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
-
Wang, W. and Kollman, P.A. 2001. Computational study of protein specificity: The molecular basis of HIV-1 protease drug resistance. Proc. Natl. Acad. Sci. 98: 14937-14942.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 14937-14942
-
-
Wang, W.1
Kollman, P.A.2
-
37
-
-
0036298514
-
Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
-
Zoete, V., Michielin, O., and Karplus, M. 2002. Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility. J. Mol. Biol. 315: 21-52.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 21-52
-
-
Zoete, V.1
Michielin, O.2
Karplus, M.3
|