-
2
-
-
0005241362
-
Active Human Immunodeficiency Virus Protease Is Required for Viral Infectivity
-
Kohl NE, Emini EA, Schleif WA, Davis LJ, Heimbach JC, et al. (1988) Active Human Immunodeficiency Virus Protease Is Required for Viral Infectivity. Proceedings of the National Academy of Sciences of the United States of America 85: 4686-4690.
-
(1988)
Proceedings of the National Academy of Sciences of the United States of America
, 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
-
3
-
-
0037028049
-
Relationships between structure and interaction kinetics for HIV-1 protease inhibitors
-
Markgren PO, Schaal W, Hamalainen M, Karlen A, Hallberg A, et al. (2002) Relationships between structure and interaction kinetics for HIV-1 protease inhibitors. Journal of Medicinal Chemistry 45: 5430-5439.
-
(2002)
Journal of Medicinal Chemistry
, vol.45
, pp. 5430-5439
-
-
Markgren, P.O.1
Schaal, W.2
Hamalainen, M.3
Karlen, A.4
Hallberg, A.5
-
4
-
-
0034483901
-
Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
-
Scott WRP, Schiffer CA, (2000) Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 8: 1259-1265.
-
(2000)
Structure
, vol.8
, pp. 1259-1265
-
-
Scott, W.R.P.1
Schiffer, C.A.2
-
5
-
-
26444548978
-
Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease
-
Hamelberg D, McCammon JA, (2005) Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. Journal of the American Chemical Society 127: 13778-13779.
-
(2005)
Journal of the American Chemical Society
, vol.127
, pp. 13778-13779
-
-
Hamelberg, D.1
McCammon, J.A.2
-
6
-
-
24344438610
-
A coarse grained model for the dynamics of flap opening in HIV-1 protease
-
Tozzini V, McCammon JA, (2005) A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chemical Physics Letters 413: 123-128.
-
(2005)
Chemical Physics Letters
, vol.413
, pp. 123-128
-
-
Tozzini, V.1
McCammon, J.A.2
-
7
-
-
32244437816
-
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
-
Hornak V, Okur A, Rizzo RC, Simmerling C, (2006) HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 103: 915-920.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 915-920
-
-
Hornak, V.1
Okur, A.2
Rizzo, R.C.3
Simmerling, C.4
-
8
-
-
67249128279
-
Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors
-
Li DC, Liu MS, Ji BH, Hwang K, Huang YG, (2009) Coarse-grained molecular dynamics of ligands binding into protein: The case of HIV-1 protease inhibitors. Journal of Chemical Physics 130: 215102.
-
(2009)
Journal of Chemical Physics
, vol.130
, pp. 215102
-
-
Li, D.C.1
Liu, M.S.2
Ji, B.H.3
Hwang, K.4
Huang, Y.G.5
-
9
-
-
65249108700
-
Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics
-
Wiley AP, Williams SL, Essex JW, (2009) Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics. Journal of Chemical Theory and Computation 5: 1117-1128.
-
(2009)
Journal of Chemical Theory and Computation
, vol.5
, pp. 1117-1128
-
-
Wiley, A.P.1
Williams, S.L.2
Essex, J.W.3
-
10
-
-
77749305127
-
Crucial Roles of the Subnanosecond Local Dynamics of the Flap Tips in the Global Conformational Changes of HIV-1 Protease
-
Li DC, Ji BH, Hwang K, Huang YG, (2010) Crucial Roles of the Subnanosecond Local Dynamics of the Flap Tips in the Global Conformational Changes of HIV-1 Protease. Journal of Physical Chemistry B 114: 3060-3069.
-
(2010)
Journal of Physical Chemistry B
, vol.114
, pp. 3060-3069
-
-
Li, D.C.1
Ji, B.H.2
Hwang, K.3
Huang, Y.G.4
-
11
-
-
77749266872
-
Coarse grained modeling of biopolymers and proteins: methods and applications
-
Li DC, Ji BH, Hwang KC, Huang YG, (2009) Coarse grained modeling of biopolymers and proteins: methods and applications. International Journal of Applied Mechanics 1: 113-136.
-
(2009)
International Journal of Applied Mechanics
, vol.1
, pp. 113-136
-
-
Li, D.C.1
Ji, B.H.2
Hwang, K.C.3
Huang, Y.G.4
-
12
-
-
33847126878
-
Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations
-
Chang CEA, Trylska J, Tozzini V, McCammon JA, (2007) Binding pathways of ligands to HIV-1 protease: Coarse-grained and atomistic simulations. Chemical Biology & Drug Design 69: 5-13.
-
(2007)
Chemical Biology & Drug Design
, vol.69
, pp. 5-13
-
-
Chang, C.E.A.1
Trylska, J.2
Tozzini, V.3
McCammon, J.A.4
-
13
-
-
69049084558
-
Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations
-
Pietrucci F, Marinelli F, Carloni P, Laio A, (2009) Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations. Journal of the American Chemical Society 131: 11811-11818.
-
(2009)
Journal of the American Chemical Society
, vol.131
, pp. 11811-11818
-
-
Pietrucci, F.1
Marinelli, F.2
Carloni, P.3
Laio, A.4
-
14
-
-
77956295819
-
Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: Atomistic and coarse-grained simulations
-
Cheng Y, Li DC, Ji BH, Shi XH, Gao HJ, (2010) Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: Atomistic and coarse-grained simulations. Journal of Molecular Graphics & Modelling 29: 171-177.
-
(2010)
Journal of Molecular Graphics & Modelling
, vol.29
, pp. 171-177
-
-
Cheng, Y.1
Li, D.C.2
Ji, B.H.3
Shi, X.H.4
Gao, H.J.5
-
15
-
-
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 LL, Tisdale M, et al. (1996) Human immunodeficiency virus- Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. Journal of Biological Chemistry 271: 33231-33235.
-
(1996)
Journal of Biological Chemistry
, vol.271
, pp. 33231-33235
-
-
Maschera, B.1
Darby, G.2
Palu, G.3
Wright, L.L.4
Tisdale, M.5
-
16
-
-
34250380707
-
HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics
-
Trylska J, Tozzini V, Chang CA, McCammon JA, (2007) HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophysical Journal 92: 4179-4187.
-
(2007)
Biophysical Journal
, vol.92
, pp. 4179-4187
-
-
Trylska, J.1
Tozzini, V.2
Chang, C.A.3
McCammon, J.A.4
-
17
-
-
37349127373
-
Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site
-
Sadiq AK, Wan S, Coveney PV, (2007) Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site. Biochemistry 46: 14865-14877.
-
(2007)
Biochemistry
, vol.46
, pp. 14865-14877
-
-
Sadiq, A.K.1
Wan, S.2
Coveney, P.V.3
-
18
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force
-
Grubmuller H, Heymann B, Tavan P, (1996) Ligand binding: Molecular mechanics calculation of the streptavidin biotin rupture force. Science 271: 997-999.
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmuller, H.1
Heymann, B.2
Tavan, P.3
-
19
-
-
48749094946
-
Force-based analysis of multidimensional energy landscapes: Application of dynamic force spectroscopy and steered molecular dynamics simulations to an antibody fragment-peptide complex
-
Morfill J, Neumann J, Blank K, Steinbach U, Puchner EM, et al. (2008) Force-based analysis of multidimensional energy landscapes: Application of dynamic force spectroscopy and steered molecular dynamics simulations to an antibody fragment-peptide complex. Journal of Molecular Biology 381: 1253-1266.
-
(2008)
Journal of Molecular Biology
, vol.381
, pp. 1253-1266
-
-
Morfill, J.1
Neumann, J.2
Blank, K.3
Steinbach, U.4
Puchner, E.M.5
-
20
-
-
70350023195
-
The Effect of Different Force Applications on the Protein-Protein Complex Barnase-Barstar
-
Neumann J, Gottschalk KE, (2009) The Effect of Different Force Applications on the Protein-Protein Complex Barnase-Barstar. Biophysical Journal 97: 1687-1699.
-
(2009)
Biophysical Journal
, vol.97
, pp. 1687-1699
-
-
Neumann, J.1
Gottschalk, K.E.2
-
21
-
-
0031848099
-
Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation
-
Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K, (1998) Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophysical Journal 75: 662-671.
-
(1998)
Biophysical Journal
, vol.75
, pp. 662-671
-
-
Lu, H.1
Isralewitz, B.2
Krammer, A.3
Vogel, V.4
Schulten, K.5
-
22
-
-
75749150524
-
Assessing the Stability of Alzheimer's Amyloid Protofibrils Using Molecular Dynamics
-
Lemkul JA, Bevan DR, (2010) Assessing the Stability of Alzheimer's Amyloid Protofibrils Using Molecular Dynamics. Journal of Physical Chemistry B 114: 1652-1660.
-
(2010)
Journal of Physical Chemistry B
, vol.114
, pp. 1652-1660
-
-
Lemkul, J.A.1
Bevan, D.R.2
-
24
-
-
23744478437
-
Free energy surfaces from single-molecule force spectroscopy
-
Hummer G, Szabo A, (2005) Free energy surfaces from single-molecule force spectroscopy. Accounts of Chemical Research 38: 504-513.
-
(2005)
Accounts of Chemical Research
, vol.38
, pp. 504-513
-
-
Hummer, G.1
Szabo, A.2
-
25
-
-
0141816804
-
Beyond the conventional description of dynamic force spectroscopy of adhesion bonds
-
Dudko OK, Filippov AE, Klafter J, Urbakh M, (2003) Beyond the conventional description of dynamic force spectroscopy of adhesion bonds. Proceedings of the National Academy of Sciences of the United States of America 100: 11378-11381.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, pp. 11378-11381
-
-
Dudko, O.K.1
Filippov, A.E.2
Klafter, J.3
Urbakh, M.4
-
26
-
-
33645004171
-
Intrinsic rates and activation free energies from single-molecule pulling experiments
-
Dudko OK, Hummer G, Szabo A, (2006) Intrinsic rates and activation free energies from single-molecule pulling experiments. Physical Review Letters 96: 108101.
-
(2006)
Physical Review Letters
, vol.96
, pp. 108101
-
-
Dudko, O.K.1
Hummer, G.2
Szabo, A.3
-
27
-
-
57349124448
-
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments
-
Dudko OK, Hummer G, Szabo A, (2008) Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proceedings of the National Academy of Sciences of the United States of America 105: 15755-15760.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 15755-15760
-
-
Dudko, O.K.1
Hummer, G.2
Szabo, A.3
-
28
-
-
0037036070
-
Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
-
Liphardt J, Dumont S, Smith SB, Tinoco I, Bustamante C, (2002) Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science 296: 1832-1835.
-
(2002)
Science
, vol.296
, pp. 1832-1835
-
-
Liphardt, J.1
Dumont, S.2
Smith, S.B.3
Tinoco, I.4
Bustamante, C.5
-
29
-
-
24644450199
-
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies
-
Collin D, Ritort F, Jarzynski C, Smith SB, Tinoco I, et al. (2005) Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies. Nature 437: 231-234.
-
(2005)
Nature
, vol.437
, pp. 231-234
-
-
Collin, D.1
Ritort, F.2
Jarzynski, C.3
Smith, S.B.4
Tinoco, I.5
-
30
-
-
33751579133
-
Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality
-
West DK, Olmsted PD, Paci E, (2006) Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality. Journal of Chemical Physics 125: 204910.
-
(2006)
Journal of Chemical Physics
, vol.125
, pp. 204910
-
-
West, D.K.1
Olmsted, P.D.2
Paci, E.3
-
31
-
-
0342929614
-
Non-Physical Sampling Distributions in Monte-Carlo Free-Energy Estimation - Umbrella Sampling
-
Torrie GM, Valleau JP, (1977) Non-Physical Sampling Distributions in Monte-Carlo Free-Energy Estimation- Umbrella Sampling. Journal of Computational Physics 23: 187-199.
-
(1977)
Journal of Computational Physics
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
32
-
-
0043222419
-
Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor
-
Backbro K, Lowgren S, Osterlund K, Atepo J, Unge T, et al. (1997) Unexpected binding mode of a cyclic sulfamide HIV-1 protease inhibitor. Journal of Medicinal Chemistry 40: 898-902.
-
(1997)
Journal of Medicinal Chemistry
, vol.40
, pp. 898-902
-
-
Backbro, K.1
Lowgren, S.2
Osterlund, K.3
Atepo, J.4
Unge, T.5
-
33
-
-
0028057975
-
Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as Hiv Protease Inhibitors
-
Lam PYS, Jadhav PK, Eyermann CJ, Hodge CN, Ru Y, et al. (1994) Rational Design of Potent, Bioavailable, Nonpeptide Cyclic Ureas as Hiv Protease Inhibitors. Science 263: 380-384.
-
(1994)
Science
, vol.263
, pp. 380-384
-
-
Lam, P.Y.S.1
Jadhav, P.K.2
Eyermann, C.J.3
Hodge, C.N.4
Ru, Y.5
-
34
-
-
0028968902
-
Abt-538 Is a Potent Inhibitor of Human-Immunodeficiency-Virus Protease and Has High Oral Bioavailability in Humans
-
Kempf DJ, Marsh KC, Denissen JF, McDonald E, Vasavanonda S, et al. (1995) Abt-538 Is a Potent Inhibitor of Human-Immunodeficiency-Virus Protease and Has High Oral Bioavailability in Humans. Proceedings of the National Academy of Sciences of the United States of America 92: 2484-2488.
-
(1995)
Proceedings of the National Academy of Sciences of the United States of America
, vol.92
, pp. 2484-2488
-
-
Kempf, D.J.1
Marsh, K.C.2
Denissen, J.F.3
McDonald, E.4
Vasavanonda, S.5
-
35
-
-
0028114966
-
Nmr and X-Ray Evidence That the Hiv Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Nonpeptide Cyclic Urea-Based Inhibitor
-
Yamazaki T, Nicholson LK, Torchia DA, Wingfield P, Stahl SJ, et al. (1994) Nmr and X-Ray Evidence That the Hiv Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Nonpeptide Cyclic Urea-Based Inhibitor. Journal of the American Chemical Society 116: 10791-10792.
-
(1994)
Journal of the American Chemical Society
, vol.116
, pp. 10791-10792
-
-
Yamazaki, T.1
Nicholson, L.K.2
Torchia, D.A.3
Wingfield, P.4
Stahl, S.J.5
-
36
-
-
40549107752
-
Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
-
Wittayanarakul K, Hannongbua S, Feig M, (2008) Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. Journal of Computational Chemistry 29: 673-685.
-
(2008)
Journal of Computational Chemistry
, vol.29
, pp. 673-685
-
-
Wittayanarakul, K.1
Hannongbua, S.2
Feig, M.3
-
37
-
-
0035789518
-
GROMACS 3.0: a package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D, (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. Journal of Molecular Modeling 7: 306-317.
-
(2001)
Journal of Molecular Modeling
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
38
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
Sorin EJ, Pande VS, (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal 88: 2472-2493.
-
(2005)
Biophysical Journal
, vol.88
, pp. 2472-2493
-
-
Sorin, E.J.1
Pande, V.S.2
-
39
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang JM, Wolf RM, Caldwell JW, Kollman PA, Case DA, (2004) Development and testing of a general amber force field. Journal of Computational Chemistry 25: 1157-1174.
-
(2004)
Journal of Computational Chemistry
, vol.25
, pp. 1157-1174
-
-
Wang, J.M.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
40
-
-
0001041959
-
Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method
-
Jakalian A, Bush BL, Jack DB, Bayly CI, (2000) Fast, efficient generation of high-quality atomic Charges. AM1-BCC model: I. Method. Journal of Computational Chemistry 21: 132-146.
-
(2000)
Journal of Computational Chemistry
, vol.21
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
41
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, et al. (2005) The Amber biomolecular simulation programs. Journal of Computational Chemistry 26: 1668-1688.
-
(2005)
Journal of Computational Chemistry
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
-
42
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, et al. (1995) A Smooth Particle Mesh Ewald Method. Journal of Chemical Physics 103: 8577-8593.
-
(1995)
Journal of Chemical Physics
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
-
43
-
-
38749123962
-
P-LINCS: A parallel linear constraint solver for molecular simulation
-
Hess B, (2008) P-LINCS: A parallel linear constraint solver for molecular simulation. Journal of Chemical Theory and Computation 4: 116-122.
-
(2008)
Journal of Chemical Theory and Computation
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
44
-
-
84986519238
-
The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. 1. the Method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM, (1992) The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. 1. the Method. Journal of Computational Chemistry 13: 1011-1021.
-
(1992)
Journal of Computational Chemistry
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
45
-
-
70349662344
-
Nanomechanical properties of vimentin intermediate filament dimers
-
Qin Z, Kreplak L, Buehler MJ, (2009) Nanomechanical properties of vimentin intermediate filament dimers. Nanotechnology 20.
-
(2009)
Nanotechnology
, vol.20
-
-
Qin, Z.1
Kreplak, L.2
Buehler, M.J.3
-
46
-
-
0031001349
-
Dynamic strength of molecular adhesion bonds
-
Evans E, Ritchie K, (1997) Dynamic strength of molecular adhesion bonds. Biophysical Journal 72: 1541-1555.
-
(1997)
Biophysical Journal
, vol.72
, pp. 1541-1555
-
-
Evans, E.1
Ritchie, K.2
-
47
-
-
33646172749
-
Coiled-coil nanomechanics and uncoiling and unfolding of the superhelix and alpha-helices of myosin
-
Root DD, Yadavalli VK, Forbes JG, Wang K, (2006) Coiled-coil nanomechanics and uncoiling and unfolding of the superhelix and alpha-helices of myosin. Biophysical Journal 90: 2852-2866.
-
(2006)
Biophysical Journal
, vol.90
, pp. 2852-2866
-
-
Root, D.D.1
Yadavalli, V.K.2
Forbes, J.G.3
Wang, K.4
-
48
-
-
77952844866
-
Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors
-
Colizzi F, Perozzo R, Scapozza L, Recanatini M, Cavalli A, (2010) Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors. Journal of the American Chemical Society 132: 7361-7371.
-
(2010)
Journal of the American Chemical Society
, vol.132
, pp. 7361-7371
-
-
Colizzi, F.1
Perozzo, R.2
Scapozza, L.3
Recanatini, M.4
Cavalli, A.5
-
49
-
-
43449096360
-
Asymptotic strength limit of hydrogen-bond assemblies in proteins at vanishing pulling rates
-
Keten S, Buehler MJ, (2008) Asymptotic strength limit of hydrogen-bond assemblies in proteins at vanishing pulling rates. Physical Review Letters 100: 198301.
-
(2008)
Physical Review Letters
, vol.100
, pp. 198301
-
-
Keten, S.1
Buehler, M.J.2
-
50
-
-
77949943700
-
Nanoconfinement controls stiffness, strength and mechanical toughness of beta-sheet crystals in silk
-
Keten S, Xu ZP, Ihle B, Buehler MJ, (2010) Nanoconfinement controls stiffness, strength and mechanical toughness of beta-sheet crystals in silk. Nature Materials 9: 359-367.
-
(2010)
Nature Materials
, vol.9
, pp. 359-367
-
-
Keten, S.1
Xu, Z.P.2
Ihle, B.3
Buehler, M.J.4
-
51
-
-
78651432266
-
Cooperative deformation of hydrogen bonds in beta-strands and beta-sheet nanocrystals
-
Zhao Q, Buehler MJ, (2010) Cooperative deformation of hydrogen bonds in beta-strands and beta-sheet nanocrystals. Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) 86: 061906.
-
(2010)
Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)
, vol.86
, pp. 061906
-
-
Zhao, Q.1
Buehler, M.J.2
-
52
-
-
0004216822
-
Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis
-
Wiley-VCH: New York
-
Copeland RA, (2000) Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis. Wiley-VCH: New York.
-
(2000)
-
-
Copeland, R.A.1
-
53
-
-
0026702928
-
Two-Step Binding Mechanism for Hiv Protease Inhibitors
-
Furfine ES, Dsouza E, Ingold KJ, Leban JJ, Spector T, et al. (1992) Two-Step Binding Mechanism for Hiv Protease Inhibitors. Biochemistry 31: 7886-7891.
-
(1992)
Biochemistry
, vol.31
, pp. 7886-7891
-
-
Furfine, E.S.1
Dsouza, E.2
Ingold, K.J.3
Leban, J.J.4
Spector, T.5
-
54
-
-
33644948688
-
HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state
-
Hornak V, Okur A, Rizzo RC, Simmerling C, (2006) HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. Journal of the American Chemical Society 128: 2812-2813.
-
(2006)
Journal of the American Chemical Society
, vol.128
, pp. 2812-2813
-
-
Hornak, V.1
Okur, A.2
Rizzo, R.C.3
Simmerling, C.4
-
55
-
-
33744730369
-
Closing of the flaps of HIV-1 protease induced by substrate binding: A model of a flap closing mechanism in retroviral aspartic proteases
-
Toth G, Borics A, (2006) Closing of the flaps of HIV-1 protease induced by substrate binding: A model of a flap closing mechanism in retroviral aspartic proteases. Biochemistry 45: 6606-6614.
-
(2006)
Biochemistry
, vol.45
, pp. 6606-6614
-
-
Toth, G.1
Borics, A.2
-
56
-
-
0039077591
-
Chemical relaxation in molecular biology;
-
In: Pecht I, Rigler R, editors, Berlin, Springer-Verlag
-
Pecht I, Lancet D, (1977) Chemical relaxation in molecular biology; In: Pecht I, Rigler R, editors. Berlin Springer-Verlag.
-
(1977)
-
-
Pecht, I.1
Lancet, D.2
-
57
-
-
0038650860
-
Kinetics from nonequilibrium single-molecule pulling experiments
-
Hummer G, Szabo A, (2003) Kinetics from nonequilibrium single-molecule pulling experiments. Biophysical Journal 85: 5-15.
-
(2003)
Biophysical Journal
, vol.85
, pp. 5-15
-
-
Hummer, G.1
Szabo, A.2
-
58
-
-
0018101150
-
Models for Specific Adhesion of Cells to Cells
-
Bell GI, (1978) Models for Specific Adhesion of Cells to Cells. Science 200: 618-627.
-
(1978)
Science
, vol.200
, pp. 618-627
-
-
Bell, G.I.1
-
59
-
-
4243754128
-
Nonequilibrium equality for free energy differences
-
Jarzynski C, (1997) Nonequilibrium equality for free energy differences. Physical Review Letters 78: 2690-2693.
-
(1997)
Physical Review Letters
, vol.78
, pp. 2690-2693
-
-
Jarzynski, C.1
-
60
-
-
33847285434
-
Application of Jarzynski's equality in simple versus complex systems
-
Bastug T, Kuyucak S, (2007) Application of Jarzynski's equality in simple versus complex systems. Chemical Physics Letters 436: 383-387.
-
(2007)
Chemical Physics Letters
, vol.436
, pp. 383-387
-
-
Bastug, T.1
Kuyucak, S.2
-
61
-
-
36749062973
-
Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains
-
Ackbarow T, Chen X, Keten S, Buehler MJ, (2007) Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains. Proceedings of the National Academy of Sciences of the United States of America 104: 16410-16415.
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, pp. 16410-16415
-
-
Ackbarow, T.1
Chen, X.2
Keten, S.3
Buehler, M.J.4
-
62
-
-
0242363173
-
Energetics of hydrogen bonds in peptides
-
Sheu SY, Yang DY, Selzle HL, Schlag EW, (2003) Energetics of hydrogen bonds in peptides. Proceedings of the National Academy of Sciences of the United States of America 100: 12683-12687.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, pp. 12683-12687
-
-
Sheu, S.Y.1
Yang, D.Y.2
Selzle, H.L.3
Schlag, E.W.4
-
63
-
-
15644376141
-
Cyclic HIV-1 protease inhibitors derived from mannitol: Synthesis, inhibitory potencies, and computational predictions of binding affinities
-
Hulten J, Bonham NM, Nillroth U, Hansson T, Zuccarello G, et al. (1997) Cyclic HIV-1 protease inhibitors derived from mannitol: Synthesis, inhibitory potencies, and computational predictions of binding affinities. Journal of Medicinal Chemistry 40: 885-897.
-
(1997)
Journal of Medicinal Chemistry
, vol.40
, pp. 885-897
-
-
Hulten, J.1
Bonham, N.M.2
Nillroth, U.3
Hansson, T.4
Zuccarello, G.5
-
64
-
-
15444345861
-
Molecular recognition of cyclic urea HIV-1 protease inhibitors
-
Ala PJ, DeLoskey RJ, Huston EE, Jadhav PK, Lam PYS, et al. (1998) Molecular recognition of cyclic urea HIV-1 protease inhibitors. Journal of Biological Chemistry 273: 12325-12331.
-
(1998)
Journal of Biological Chemistry
, vol.273
, pp. 12325-12331
-
-
Ala, P.J.1
DeLoskey, R.J.2
Huston, E.E.3
Jadhav, P.K.4
Lam, P.Y.S.5
|