-
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. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 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. The protein data bank. Nucleic Acids Res. 28 (2000) 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
-
-
33744940504
-
Gated binding of ligands to hiv-1 protease: Brownian dynamics simulations in a coarse-grained model
-
Chang C., Shen T., Trylska J., Tozzini V., and McCammon J.A. Gated binding of ligands to hiv-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys. J. 90 (2006) 3880-3885
-
(2006)
Biophys. J.
, vol.90
, pp. 3880-3885
-
-
Chang, C.1
Shen, T.2
Trylska, J.3
Tozzini, V.4
McCammon, J.A.5
-
5
-
-
0028958868
-
Flap opening in HIV-1 protease simulated by activated molecular dynamics
-
Collins J.R., Burt S.K., and Erickson J.W. Flap opening in HIV-1 protease simulated by activated molecular dynamics. Nat. Struct. Biol. 2 (1995) 334-338
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 334-338
-
-
Collins, J.R.1
Burt, S.K.2
Erickson, J.W.3
-
6
-
-
0036846898
-
New anti-HIV agents and targets
-
de Clercq E. New anti-HIV agents and targets. Med. Res. Rev. 22 (2002) 531-565
-
(2002)
Med. Res. Rev.
, vol.22
, pp. 531-565
-
-
de Clercq, E.1
-
7
-
-
33750652614
-
Brownian dynamics with hydrodynamic interactions
-
Ermak D.L., and McCammon J.A. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69 (1978) 1352-1360
-
(1978)
J. Chem. Phys.
, vol.69
, pp. 1352-1360
-
-
Ermak, D.L.1
McCammon, J.A.2
-
8
-
-
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. 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 (2002) 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
-
9
-
-
26444548978
-
Fast peptidyl cis-trans isomerization within the flexible gly-rich flaps of HIV-1 protease
-
Hamelberg D., and McCammon J.A. Fast peptidyl cis-trans isomerization within the flexible gly-rich flaps of HIV-1 protease. J. Am. Chem. Soc. 127 (2005) 13778-13779
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 13778-13779
-
-
Hamelberg, D.1
McCammon, J.A.2
-
10
-
-
32244437816
-
HIV-1 protease flaps spontaneously open and re-close in molecular dynamics simulations
-
Hornak V., Okur A., Rizzo R.C., and Simmerling C. HIV-1 protease flaps spontaneously open and re-close in molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 103 (2006) 915-920
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 915-920
-
-
Hornak, V.1
Okur, A.2
Rizzo, R.C.3
Simmerling, C.4
-
12
-
-
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. Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 7 (1999) 1047-1055
-
(1999)
Structure
, vol.7
, pp. 1047-1055
-
-
Ishima, R.1
Freedberg, D.I.2
Wang, Y.X.3
Louis, J.M.4
Torchia, D.A.5
-
13
-
-
0005241362
-
Active human immunodeficiency virus protease is required for viral infectivity
-
Kohl N.E., Emini E.A., Schleif W.A., Davis L.J., Heimbach J.C., Dixon R.A., Scolnick E.M., and Sigal I.S. Active human immunodeficiency virus protease is required for viral infectivity. Proc. Natl. Acad. Sci. USA 85 (1988) 4686-4690
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 4686-4690
-
-
Kohl, N.E.1
Emini, E.A.2
Schleif, W.A.3
Davis, L.J.4
Heimbach, J.C.5
Dixon, R.A.6
Scolnick, E.M.7
Sigal, I.S.8
-
14
-
-
0041922335
-
HIV-1 protease inhibitors: A comparative QSAR analysis
-
Kurup A., Mekapati S.B., Garg R., and Hansch C. HIV-1 protease inhibitors: A comparative QSAR analysis. Curr. Med. Chem. 10 17 (2003) 1679-1688
-
(2003)
Curr. Med. Chem.
, vol.10
, Issue.17
, pp. 1679-1688
-
-
Kurup, A.1
Mekapati, S.B.2
Garg, R.3
Hansch, C.4
-
15
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory
-
Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory. J. Mol. Model. 7 (2001) 306-317
-
(2001)
J. Mol. Model.
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
16
-
-
0026869597
-
Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N-methylamide
-
Loncharich R.J., Brooks B.R., and Pastor R.W. Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N-methylamide. Biopolymers 32 (1992) 523-535
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
17
-
-
28844446162
-
Wide open 1.3 Å structure of a multi-drug resistant HIV-1 protease represents a novel drug target
-
Martin P., Vickrey J.F., Proteasa G., Jimenez Y.L., Wawrzak Z., Winters M.A., Merigan T.C., and Kovari L.C. Wide open 1.3 Å structure of a multi-drug resistant HIV-1 protease represents a novel drug target. Structure 13 (2005) 887-1895
-
(2005)
Structure
, vol.13
, pp. 887-1895
-
-
Martin, P.1
Vickrey, J.F.2
Proteasa, G.3
Jimenez, Y.L.4
Wawrzak, Z.5
Winters, M.A.6
Merigan, T.C.7
Kovari, L.C.8
-
18
-
-
33646536078
-
The influence of macromolecular crowding on hiv-1 protease internal dynamics
-
Minh D.D.L., Chang C., Trylska J., Tozzini V., and McCammon J.A. The influence of macromolecular crowding on hiv-1 protease internal dynamics. J. Am. Chem. Soc. 128 (2006) 6006-6007
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 6006-6007
-
-
Minh, D.D.L.1
Chang, C.2
Trylska, J.3
Tozzini, V.4
McCammon, J.A.5
-
19
-
-
11244269735
-
Interactive essential dynamics
-
Mongan J. Interactive essential dynamics. J. Comput. Aided Mol. Des. 18 (2004) 433-436
-
(2004)
J. Comput. Aided Mol. Des.
, vol.18
, pp. 433-436
-
-
Mongan, J.1
-
20
-
-
0028921302
-
Flexibility and function in HIV-1 protease
-
Nicholson L.K., Yamazaki T., Torchia D.A., Grzesiek S., Bax A., Stahl S.J., Kaufman J.D., Wingfield P.T., Lam P.Y.S., Jadhav P.K., Hodge C.N., Domaille P.J., and Chang C.H. Flexibility and function in HIV-1 protease. Nat. Struct. Biol. 2 (1995) 274-280
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 274-280
-
-
Nicholson, L.K.1
Yamazaki, T.2
Torchia, D.A.3
Grzesiek, S.4
Bax, A.5
Stahl, S.J.6
Kaufman, J.D.7
Wingfield, P.T.8
Lam, P.Y.S.9
Jadhav, P.K.10
Hodge, C.N.11
Domaille, P.J.12
Chang, C.H.13
-
21
-
-
1842454635
-
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
-
Perryman A.L., Lin J.-H., and McCammon J.A. HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci. 13 (2004) 1108-1123
-
(2004)
Protein Sci.
, vol.13
, pp. 1108-1123
-
-
Perryman, A.L.1
Lin, J.-H.2
McCammon, J.A.3
-
22
-
-
33744491862
-
Restrained molecular dynamics simulations of hiv-1 protease: the first step in validating a new target for drug design
-
Perryman A.L., Lin J.-H., and McCammon J.A. Restrained molecular dynamics simulations of hiv-1 protease: the first step in validating a new target for drug design. Biopolymers 82 (2006) 272-284
-
(2006)
Biopolymers
, vol.82
, pp. 272-284
-
-
Perryman, A.L.1
Lin, J.-H.2
McCammon, J.A.3
-
23
-
-
0035956886
-
Recent improvements in prediction of protein structure by global optimization of a potential energy function
-
Pillardy J., Czaplewski C., Liwo A., Lee J., Ripoll D.R., Kazmierkiewicz R., Oldziej S., Wedemeyer W.J., Gibson K.D., Arnautova Y.A., Saunders J., Ye Y.-J., and Sheraga H.A. Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc. Natl. Acad. Sci. USA 98 (2001) 2329-2333
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 2329-2333
-
-
Pillardy, J.1
Czaplewski, C.2
Liwo, A.3
Lee, J.4
Ripoll, D.R.5
Kazmierkiewicz, R.6
Oldziej, S.7
Wedemeyer, W.J.8
Gibson, K.D.9
Arnautova, Y.A.10
Saunders, J.11
Ye, Y.-J.12
Sheraga, H.A.13
-
24
-
-
0042783950
-
Deriving effective mesoscale potentials from atomistic simulations
-
Reith D., Pütz M., and Müller-Plathe F. Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 24 (2003) 1624-1636
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1624-1636
-
-
Reith, D.1
Pütz, M.2
Müller-Plathe, F.3
-
25
-
-
0030781040
-
Residue-residue mean-force potentials for protein structure recognition
-
Reva B.A., Finkelstein A.V., Sanner M.F., and Olson A.J. Residue-residue mean-force potentials for protein structure recognition. Protein Eng. 10 (1997) 865-876
-
(1997)
Protein Eng.
, vol.10
, pp. 865-876
-
-
Reva, B.A.1
Finkelstein, A.V.2
Sanner, M.F.3
Olson, A.J.4
-
26
-
-
0034483901
-
Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
-
Scott W.R.P., and Schiffer C.A. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 8 (2000) 1259-1265
-
(2000)
Structure
, vol.8
, pp. 1259-1265
-
-
Scott, W.R.P.1
Schiffer, C.A.2
-
27
-
-
0035913754
-
Atomistic brownian dynamics simulation of peptide phosphorylation
-
Shen T.Y., Wong C.F., and McCammon J.A. Atomistic brownian dynamics simulation of peptide phosphorylation. J. Am. Chem. Soc. 123 (2001) 9107-9111
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 9107-9111
-
-
Shen, T.Y.1
Wong, C.F.2
McCammon, J.A.3
-
28
-
-
1642310506
-
Kinetic and thermodynamic characterization of hiv-1 protease inhibitors
-
Shuman C.F., Hämäläinen M.D., and Danielson U.D. Kinetic and thermodynamic characterization of hiv-1 protease inhibitors. J. Mol. Recognit. 17 (2004) 106-119
-
(2004)
J. Mol. Recognit.
, vol.17
, pp. 106-119
-
-
Shuman, C.F.1
Hämäläinen, M.D.2
Danielson, U.D.3
-
29
-
-
0030175155
-
DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package
-
Smith W., and Forester T.R. DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package. J. Mol. Graph. 14 (1996) 136-141
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 136-141
-
-
Smith, W.1
Forester, T.R.2
-
30
-
-
17044393884
-
Coarse grained models for proteins
-
Tozzini V. Coarse grained models for proteins. Curr. Opin. Struct. Biol. 15 (2005) 144-150
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
31
-
-
24344438610
-
A coarse grained model for the dynamics of flap opening in HIV-1 protease
-
Tozzini V., and McCammon J.A. A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem. Phys. Lett. 413 (2005) 123-128
-
(2005)
Chem. Phys. Lett.
, vol.413
, pp. 123-128
-
-
Tozzini, V.1
McCammon, J.A.2
-
32
-
-
33846213672
-
Mapping all-atom models onto one-bead coarse grained models: general properties and applications to a minimal polypeptide model
-
Tozzini V., Rocchia W., and McCammon J.A. Mapping all-atom models onto one-bead coarse grained models: general properties and applications to a minimal polypeptide model. J. Chem. Theory Comput. 2 (2006) 667-673
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 667-673
-
-
Tozzini, V.1
Rocchia, W.2
McCammon, J.A.3
-
33
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
Trylska J., Tozzini V., and McCammon J.A. Exploring global motions and correlations in the ribosome. Biophys. J. 89 (2005) 1455-1463
-
(2005)
Biophys. J.
, vol.89
, pp. 1455-1463
-
-
Trylska, J.1
Tozzini, V.2
McCammon, J.A.3
-
34
-
-
34548105157
-
Monte carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials
-
van Giessen A.E., and Straub J.E. Monte carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials. J. Chem. Phys. 122 (2005)
-
(2005)
J. Chem. Phys.
, vol.122
-
-
van Giessen, A.E.1
Straub, J.E.2
-
35
-
-
0036892381
-
HIVdb: a database of the structures of human immunodeficiency virus protease
-
Vondrasek J., and Wlodawer A. HIVdb: a database of the structures of human immunodeficiency virus protease. Protein Struct. Funct. Genet. 49 (2002) 429-431
-
(2002)
Protein Struct. Funct. Genet.
, vol.49
, pp. 429-431
-
-
Vondrasek, J.1
Wlodawer, A.2
-
36
-
-
0036176766
-
Rational approach to AIDS drug design through structural biology
-
Wlodawer A. Rational approach to AIDS drug design through structural biology. Annu. Rev. Med. 53 (2002) 595-614
-
(2002)
Annu. Rev. Med.
, vol.53
, pp. 595-614
-
-
Wlodawer, A.1
|