-
1
-
-
23044435317
-
Statistical and molecular dynamics studies of buried waters in globular proteins
-
Park S, Saven JG. Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 2005;60:450-46.
-
(2005)
Proteins
, vol.60
, pp. 450-446
-
-
Park, S.1
Saven, J.G.2
-
2
-
-
13244260957
-
Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase
-
Tashiro M, Stuchebrukhov AA. Thermodynamic properties of internal water molecules in the hydrophobic cavity around the catalytic center of cytochrome c oxidase. J Phys Chem B 2005;109:1015-1022.
-
(2005)
J Phys Chem B
, vol.109
, pp. 1015-1022
-
-
Tashiro, M.1
Stuchebrukhov, A.A.2
-
3
-
-
0038649076
-
Crystallographic structures of the M and N intermediates of bacteriorhodopsin: Assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base
-
Schobert B, Brown LS, Lanyi JK. Crystallographic structures of the M and N intermediates of bacteriorhodopsin: assembly of a hydrogen-bonded chain of water molecules between Asp-96 and the retinal Schiff base. J Mol Biol 2003;330:553-570.
-
(2003)
J Mol Biol
, vol.330
, pp. 553-570
-
-
Schobert, B.1
Brown, L.S.2
Lanyi, J.K.3
-
4
-
-
0033578333
-
Binding of buried structural water increases the flexibility of proteins
-
Fischer S, Verma CS. Binding of buried structural water increases the flexibility of proteins. Proc Natl Acad Sci USA 1999;96:9613-9615.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 9613-9615
-
-
Fischer, S.1
Verma, C.S.2
-
5
-
-
0035940247
-
Dissecting the vibrational entropy change on protein/ligand binding: Burial of a water
-
Fischer S, Smith JC, Verma CS. Dissecting the vibrational entropy change on protein/ligand binding: burial of a water. J Phys Chem B 2001;105:8050-8055.
-
(2001)
J Phys Chem B
, vol.105
, pp. 8050-8055
-
-
Fischer, S.1
Smith, J.C.2
Verma, C.S.3
-
6
-
-
3042592839
-
Hydration free energies and entropies for water in protein interiors
-
Olano LR, Rick SW. Hydration free energies and entropies for water in protein interiors. J Am Chem Soc 2004;126:7991-8000.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 7991-8000
-
-
Olano, L.R.1
Rick, S.W.2
-
7
-
-
1842534583
-
MHC-peptide binding is assisted by bound water molecules
-
Petrone PM, Garcia AE. MHC-peptide binding is assisted by bound water molecules. J Mol Biol 2004;338:419-435.
-
(2004)
J Mol Biol
, vol.338
, pp. 419-435
-
-
Petrone, P.M.1
Garcia, A.E.2
-
8
-
-
0027918556
-
Water: Now you see it, now you don't
-
Levitt M, Park BH. Water: now you see it, now you don't. Structure 1993;1:223-226.
-
(1993)
Structure
, vol.1
, pp. 223-226
-
-
Levitt, M.1
Park, B.H.2
-
9
-
-
0029882171
-
Structural and energetic responses to cavity-creating mutations in hydrophobic cores: Observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities
-
Buckle AM, Cramer P, Fersht AR. Structural and energetic responses to cavity-creating mutations in hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. Biochemistry 1996;35:4298-4305.
-
(1996)
Biochemistry
, vol.35
, pp. 4298-4305
-
-
Buckle, A.M.1
Cramer, P.2
Fersht, A.R.3
-
10
-
-
0033524454
-
Disordered water within a hydrophobic protein cavity visualized by X-ray crystallography
-
Yu B, Blaber M, Gronenborn AM, Clore GM, Caspar DLD. Disordered water within a hydrophobic protein cavity visualized by X-ray crystallography. Proc Natl Acad Sci USA 1999;96:103-108.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 103-108
-
-
Yu, B.1
Blaber, M.2
Gronenborn, A.M.3
Clore, G.M.4
Caspar, D.L.D.5
-
11
-
-
0037974485
-
Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain
-
Guo W, Lampoudi S, Shea JE. Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. Biophys J 2003;85:61-69.
-
(2003)
Biophys J
, vol.85
, pp. 61-69
-
-
Guo, W.1
Lampoudi, S.2
Shea, J.E.3
-
12
-
-
0028093141
-
On the probability of finding a water molecule in a nonpolar cavity
-
Wolfenden R, Radzicka. On the probability of finding a water molecule in a nonpolar cavity. Science 1994;265:936-937.
-
(1994)
Science
, vol.265
, pp. 936-937
-
-
Wolfenden, R.1
Radzicka2
-
13
-
-
0029937870
-
Hydrophilicity of cavities in proteins
-
Zhang L, Hermans J. Hydrophilicity of cavities in proteins. Proteins 1996;24:433-438.
-
(1996)
Proteins
, vol.24
, pp. 433-438
-
-
Zhang, L.1
Hermans, J.2
-
14
-
-
0026189146
-
A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins
-
Wade R, Mazor M, McCammon J, Quiocho F. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers 1991;31:919-931.
-
(1991)
Biopolymers
, vol.31
, pp. 919-931
-
-
Wade, R.1
Mazor, M.2
McCammon, J.3
Quiocho, F.4
-
15
-
-
0033850087
-
High apparent dielectric constants in the interior of a protein reflect water penetration
-
Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, Stites WE, Moreno G. High apparent dielectric constants in the interior of a protein reflect water penetration. Biophysical J 2000;79:1610-1620.
-
(2000)
Biophysical J
, vol.79
, pp. 1610-1620
-
-
Dwyer, J.J.1
Gittis, A.G.2
Karp, D.A.3
Lattman, E.E.4
Spencer, D.S.5
Stites, W.E.6
Moreno, G.7
-
16
-
-
0026549038
-
Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: Pattern of primary and secondary hydration of trypsin
-
Kossiakoff AA, Sintchak MD, Shpungin J, Presta LG. Analysis of solvent structure in proteins using neutron D2O-H2O solvent maps: pattern of primary and secondary hydration of trypsin. Proteins 1992;12:223-236.
-
(1992)
Proteins
, vol.12
, pp. 223-236
-
-
Kossiakoff, A.A.1
Sintchak, M.D.2
Shpungin, J.3
Presta, L.G.4
-
17
-
-
0028921999
-
Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR
-
Ernst JA, Clubb RT, Zhou HX, Gronenborn AM, Clore GM. Demonstration of positionally disordered water within a protein hydrophobic cavity by NMR. Science 1995;267:1813-1817.
-
(1995)
Science
, vol.267
, pp. 1813-1817
-
-
Ernst, J.A.1
Clubb, R.T.2
Zhou, H.X.3
Gronenborn, A.M.4
Clore, G.M.5
-
18
-
-
0030892956
-
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules
-
Otting G, Liepinsh E, Halle B, Frey U. NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Nature 1997;85:396-404.
-
(1997)
Nature
, vol.85
, pp. 396-404
-
-
Otting, G.1
Liepinsh, E.2
Halle, B.3
Frey, U.4
-
19
-
-
0141456396
-
Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with water-NOE NMR experiments
-
Cai S, Stevens SY, Budor AP, Zuiderweg ER. Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with water-NOE NMR experiments. Biochemistry 2003;42:11100-11108.
-
(2003)
Biochemistry
, vol.42
, pp. 11100-11108
-
-
Cai, S.1
Stevens, S.Y.2
Budor, A.P.3
Zuiderweg, E.R.4
-
20
-
-
0029561720
-
Use of NMR to detect water within nonpolar protein cavities
-
Matthews BW, Morton AG, Dahlquist FW. Use of NMR to detect water within nonpolar protein cavities. Science 1995;270:1847-1848.
-
(1995)
Science
, vol.270
, pp. 1847-1848
-
-
Matthews, B.W.1
Morton, A.G.2
Dahlquist, F.W.3
-
22
-
-
21244469736
-
Molecular dynamics study of water penetration in staphylococcal nuclease
-
Damjanovic A, Garcia-Moreno B, Lattman EE, Garcia AE. Molecular dynamics study of water penetration in staphylococcal nuclease. Proteins 2005;60:433-449.
-
(2005)
Proteins
, vol.60
, pp. 433-449
-
-
Damjanovic, A.1
Garcia-Moreno, B.2
Lattman, E.E.3
Garcia, A.E.4
-
23
-
-
28044463816
-
Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
-
Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM. Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci USA 2005;102:16668-16671.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 16668-16671
-
-
Collins, M.D.1
Hummer, G.2
Quillin, M.L.3
Matthews, B.W.4
Gruner, S.M.5
-
24
-
-
0037726809
-
Water-gated mechanism of proton translocation by cytochrome c oxidase
-
Wikstrom M, Verkhovsky MI, Hummer G. Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochim Biophys Acta 2003;1604:61-65.
-
(2003)
Biochim Biophys Acta
, vol.1604
, pp. 61-65
-
-
Wikstrom, M.1
Verkhovsky, M.I.2
Hummer, G.3
-
25
-
-
14744270583
-
Protein stability and ligand binding: New paradigms from in-silico experiments
-
Verma CS, Fischer S. Protein stability and ligand binding: new paradigms from in-silico experiments. Biophys Chem 2005;115(2/3):295-302.
-
(2005)
Biophys Chem
, vol.115
, Issue.2-3
, pp. 295-302
-
-
Verma, C.S.1
Fischer, S.2
-
26
-
-
0029994817
-
Using buried water molecules to explore the energy landscape of proteins
-
Denisov VP, Peters J, Horlein HD, Halle B. Using buried water molecules to explore the energy landscape of proteins. Nat Struct Biol 1996;3:505-509.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 505-509
-
-
Denisov, V.P.1
Peters, J.2
Horlein, H.D.3
Halle, B.4
-
27
-
-
0037198650
-
Hydrophobicity: Two faces of water
-
Chandler D. Hydrophobicity: two faces of water. Nature 2002;417:491.
-
(2002)
Nature
, vol.417
, pp. 491
-
-
Chandler, D.1
-
28
-
-
0034651984
-
Water penetration and escape in proteins
-
Garcia AE, Hummer G. Water penetration and escape in proteins. Proteins 2000;38:261-272.
-
(2000)
Proteins
, vol.38
, pp. 261-272
-
-
Garcia, A.E.1
Hummer, G.2
-
29
-
-
0036606442
-
Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein
-
Bakowies D, van Gunsteren WF. Water in protein cavities: a procedure to identify internal water and exchange pathways and application to fatty acid-binding protein. Proteins 2002;47: 534-545.
-
(2002)
Proteins
, vol.47
, pp. 534-545
-
-
Bakowies, D.1
van Gunsteren, W.F.2
-
30
-
-
0035829539
-
Water conduction through the hydrophobic channel of a carbon nanotube
-
Hummer G, Rasaiah JC, Noworyta JP. Water conduction through the hydrophobic channel of a carbon nanotube. Nature 2001;414:188-190.
-
(2001)
Nature
, vol.414
, pp. 188-190
-
-
Hummer, G.1
Rasaiah, J.C.2
Noworyta, J.P.3
-
31
-
-
7244251461
-
Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands
-
Noskov SY, Berneche S, Roux B. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 2004;431:830-834.
-
(2004)
Nature
, vol.431
, pp. 830-834
-
-
Noskov, S.Y.1
Berneche, S.2
Roux, B.3
-
32
-
-
4444255998
-
Detailed hydration maps of benzene and cyclohexane reveal distinct water structures
-
Raschke TM, Levitt M. Detailed hydration maps of benzene and cyclohexane reveal distinct water structures. J Phys Chem B 2004;108:13492-13500.
-
(2004)
J Phys Chem B
, vol.108
, pp. 13492-13500
-
-
Raschke, T.M.1
Levitt, M.2
-
33
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Mod 2001;7:306-317.
-
(2001)
J Mol Mod
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
34
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin
-
Jorgensen WL, Tirado-Rives J. The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
-
(1988)
J Am Chem Soc
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
35
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys 1995;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
Lee, H.5
Pedersen, L.G.6
-
37
-
-
84986440341
-
SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto S, Kollman PA. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J Comp Chem 1992;13:952-962.
-
(1992)
J Comp Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
39
-
-
0026684043
-
A 500ps molecular dynamics simulation study of interleukin-1β in water: Correlation with nuclear magnetic resonance spectroscopy and crystallography
-
Chandrasekhar I, Clore GM, Szabo A, Gronenborn AM, Brooks BR. A 500ps molecular dynamics simulation study of interleukin-1β in water: correlation with nuclear magnetic resonance spectroscopy and crystallography. J Mol Biol 1992;226:239-250.
-
(1992)
J Mol Biol
, vol.226
, pp. 239-250
-
-
Chandrasekhar, I.1
Clore, G.M.2
Szabo, A.3
Gronenborn, A.M.4
Brooks, B.R.5
-
40
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules, Part 1. Theory and range of validity
-
Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules, Part 1. Theory and range of validity. J Am Chem Soc 1980;104:4546-4559.
-
(1980)
J Am Chem Soc
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
41
-
-
0026076090
-
Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
-
Ichiye T, Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991;11:205-217.
-
(1991)
Proteins
, vol.11
, pp. 205-217
-
-
Ichiye, T.1
Karplus, M.2
-
42
-
-
8344280383
-
Electric field and temperature effects on water in carbon nanotubes
-
Vaitheeswaran S, Rasaiah JC, Hummer G. Electric field and temperature effects on water in carbon nanotubes. J Chem Phys 2004;121:7955.
-
(2004)
J Chem Phys
, vol.121
, pp. 7955
-
-
Vaitheeswaran, S.1
Rasaiah, J.C.2
Hummer, G.3
-
43
-
-
0242364982
-
Calculation of free-energy differences from computer simulations of initial and final states
-
Hummer G, Szabo A. Calculation of free-energy differences from computer simulations of initial and final states. J Chem Phys 1996;105:2004-2010.
-
(1996)
J Chem Phys
, vol.105
, pp. 2004-2010
-
-
Hummer, G.1
Szabo, A.2
-
44
-
-
11744348751
-
Hydrophobic effects on a molecular scale
-
Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. Hydrophobic effects on a molecular scale. J Phys Chem B 1998;102:10469-10482.
-
(1998)
J Phys Chem B
, vol.102
, pp. 10469-10482
-
-
Hummer, G.1
Garde, S.2
García, A.E.3
Paulaitis, M.E.4
Pratt, L.R.5
-
45
-
-
0028986918
-
Internal mobility of the basic pancreatic trypsin inhibitor in solution: A comparison of NMR spin relaxation measurements and molecular dynamics simulations
-
Smith PE, van Schaik RC, Szyperski T, Wuthrich K, van Gunsteren WF. Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations. J Mol Biol 1995;246:356-365.
-
(1995)
J Mol Biol
, vol.246
, pp. 356-365
-
-
Smith, P.E.1
van Schaik, R.C.2
Szyperski, T.3
Wuthrich, K.4
van Gunsteren, W.F.5
-
47
-
-
0029757992
-
Thermodynamics stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
-
Roux B, Nina M, Pomes R, Smith JC. Thermodynamics stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J 1996;72:670-681.
-
(1996)
Biophys J
, vol.72
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Pomes, R.3
Smith, J.C.4
-
48
-
-
0033168381
-
Does picosecond protein dynamics have survival value?
-
Brunori M, Cutruzzola F, Savino C, Travaglini-Allocatelli C, Vallone B, Gibson QH. Does picosecond protein dynamics have survival value? Trends Biochem Sci 1999;24:253-255.
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 253-255
-
-
Brunori, M.1
Cutruzzola, F.2
Savino, C.3
Travaglini-Allocatelli, C.4
Vallone, B.5
Gibson, Q.H.6
-
49
-
-
0038472282
-
Liquid-vapor oscillations of water in hydrophobic nanopores
-
Beckstein O, Sansom MS. Liquid-vapor oscillations of water in hydrophobic nanopores. Proc Natl Acad Sci USA 2003;100:7063-7068.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 7063-7068
-
-
Beckstein, O.1
Sansom, M.S.2
-
50
-
-
0344196965
-
The interleukin 1 receptor: Ligand interactions and signal transduction
-
Auron PE. The interleukin 1 receptor: ligand interactions and signal transduction. Cytokine Growth Factor Rev 1998;9(3/4):221-237.
-
(1998)
Cytokine Growth Factor Rev
, vol.9
, Issue.3-4
, pp. 221-237
-
-
Auron, P.E.1
-
51
-
-
0036307741
-
The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus
-
Tama F, Brooks CL. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. J Mol Biol 2002;318:733-747.
-
(2002)
J Mol Biol
, vol.318
, pp. 733-747
-
-
Tama, F.1
Brooks, C.L.2
-
52
-
-
0034711314
-
X-ray crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1
-
Vigers GP, Dripps DJ, Edwards CK, III, Brandhuber BJ. X-ray crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1. J Biol Chem 2000;275:36927-36933.
-
(2000)
J Biol Chem
, vol.275
, pp. 36927-36933
-
-
Vigers, G.P.1
Dripps, D.J.2
Edwards III, C.K.3
Brandhuber, B.J.4
-
53
-
-
7444230904
-
Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations
-
Hummer G, Schotte F, Anfinrud PA. Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations. Proc Natl Acad Sci USA 2004;101:15330-15334.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 15330-15334
-
-
Hummer, G.1
Schotte, F.2
Anfinrud, P.A.3
-
55
-
-
0029905014
-
The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic catalysis
-
Shan S, Herschlag D. The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis. Proc Natl Acad Sci USA 1996;93:14474-14479.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 14474-14479
-
-
Shan, S.1
Herschlag, D.2
-
56
-
-
0035895356
-
Polar group burial contributes more to protein stability than nonpolar group burial
-
Pace CN. Polar group burial contributes more to protein stability than nonpolar group burial. Biochemistry 2001;40:310-313.
-
(2001)
Biochemistry
, vol.40
, pp. 310-313
-
-
Pace, C.N.1
-
57
-
-
7444257387
-
Efficient evaluation of binding free energy using continuum electrostatics solvation
-
Huang D, Caflisch A. Efficient evaluation of binding free energy using continuum electrostatics solvation. J Med Chem 2004;47:5791-5797.
-
(2004)
J Med Chem
, vol.47
, pp. 5791-5797
-
-
Huang, D.1
Caflisch, A.2
-
58
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of protein
-
MacKerell AD, Jr., Bashford D, Bellott M, Dunbrack RL, Jr., Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, III, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of protein. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
59
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;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
-
60
-
-
12344321689
-
Structural and energetic consequences of mutations in a solvated hydrophobic cavity
-
Adamek DH, Guerrero L, Blaber M, Caspar DLD. Structural and energetic consequences of mutations in a solvated hydrophobic cavity. J Mol Biol 2005;346:307-318.
-
(2005)
J Mol Biol
, vol.346
, pp. 307-318
-
-
Adamek, D.H.1
Guerrero, L.2
Blaber, M.3
Caspar, D.L.D.4
-
61
-
-
0042845836
-
The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin
-
Friedman R, Nachliel E, Gutman M. The role of small intraprotein cavities in the catalytic cycle of bacteriorhodopsin. Biophys J 2003;85:886-896.
-
(2003)
Biophys J
, vol.85
, pp. 886-896
-
-
Friedman, R.1
Nachliel, E.2
Gutman, M.3
-
62
-
-
23244457434
-
Molecular dynamics simulation of sperm whale myoglobin: Effects of mutations and trapped CO on the structure and dynamics of cavities
-
Bossa C, Amadei A, Daidone I, Anselmi M, Vallone B, Brunori M, Di Nola A. Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Biophys J 2005;89:465-474.
-
(2005)
Biophys J
, vol.89
, pp. 465-474
-
-
Bossa, C.1
Amadei, A.2
Daidone, I.3
Anselmi, M.4
Vallone, B.5
Brunori, M.6
Di Nola, A.7
-
63
-
-
0028409107
-
Discovery of new ligand binding pathways in myoglobin by random mutagenesis
-
Huang X, Boxer SG. Discovery of new ligand binding pathways in myoglobin by random mutagenesis. Nat Struct Biol 1994;1:226-229.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 226-229
-
-
Huang, X.1
Boxer, S.G.2
-
64
-
-
2142715470
-
Water dynamics and dewetting transitions in the small mechanosensitive channel MscS
-
Anishkin A, Sukharev S. Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. Biophys J 2004;86:2883-2895.
-
(2004)
Biophys J
, vol.86
, pp. 2883-2895
-
-
Anishkin, A.1
Sukharev, S.2
-
65
-
-
4644220261
-
Mechanism of ammonia transport by Amt/MEP/Rh: Structure of AmtB at 1.35 A
-
Khademi S, O'Connell J, III, Remis J, Robles-Colmenares Y, Miercke LJ, Stroud RM. Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Science 2004;305:1587-1594.
-
(2004)
Science
, vol.305
, pp. 1587-1594
-
-
Khademi, S.1
O'Connell III, J.2
Remis, J.3
Robles-Colmenares, Y.4
Miercke, L.J.5
Stroud, R.M.6
-
66
-
-
4143085329
-
Modulating functional loop movements: The role of highly conserved residues in the correlated loop motions
-
Gunasekaran K, Nussinov R. Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions. Chembiochem 2004;5:224-230.
-
(2004)
Chembiochem
, vol.5
, pp. 224-230
-
-
Gunasekaran, K.1
Nussinov, R.2
-
67
-
-
27144438673
-
Long-range coupling between separate docking sites in interleukin-1β
-
Heidary DK, Roy M, Daumy GO, Cong Y, Jennings PA. Long-range coupling between separate docking sites in interleukin-1β. J Mol Biol 2005;353:1187-1198.
-
(2005)
J Mol Biol
, vol.353
, pp. 1187-1198
-
-
Heidary, D.K.1
Roy, M.2
Daumy, G.O.3
Cong, Y.4
Jennings, P.A.5
-
68
-
-
33144474649
-
Solution structure of p53 core domain: Structural basis for its instability
-
Canadillas JM, Tidow H, Freund SMV, Rutherford TJ, Ang HC, Fersht AR. Solution structure of p53 core domain: structural basis for its instability. Proc Natl Acad Sci USA 2006;103:2109-2114.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 2109-2114
-
-
Canadillas, J.M.1
Tidow, H.2
Freund, S.M.V.3
Rutherford, T.J.4
Ang, H.C.5
Fersht, A.R.6
-
69
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001;98:10037-10041.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
70
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations
-
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 2004;32:665-667.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 665-667
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
|