-
1
-
-
0015518520
-
Structure of crystalline a-chymotrypsin: V. The atomic structure of tosyl-a-chymotrypsin at 2 Å resolution
-
Birktoft JJ, Blow DM. Structure of crystalline a-chymotrypsin: v. the atomic structure of tosyl-a-chymotrypsin at 2 Å resolution. J Mol Biol 1972;68:187-240.
-
(1972)
J Mol Biol
, vol.68
, pp. 187-240
-
-
Birktoft, J.J.1
Blow, D.M.2
-
2
-
-
0015895751
-
Quenching of a protein fluorescence by oxygen: Detection of structural fluctuations in proteins on the nanosecond timescale
-
Lakowicz JR, Weber G. Quenching of a protein fluorescence by oxygen: detection of structural fluctuations in proteins on the nanosecond timescale. Biochemistry 1973;12:4171-4179.
-
(1973)
Biochemistry
, vol.12
, pp. 4171-4179
-
-
Lakowicz, J.R.1
Weber, G.2
-
3
-
-
0000767837
-
Dynamics of a protein matrix revealed by fluorescence quenching
-
Eftink MR, Ghiron CA. Dynamics of a protein matrix revealed by fluorescence quenching. Proc Natl Acad Sci USA 1975;72:3290-3294.
-
(1975)
Proc Natl Acad Sci USA
, vol.72
, pp. 3290-3294
-
-
Eftink, M.R.1
Ghiron, C.A.2
-
4
-
-
0021107512
-
Interior turns in globular proteins
-
Rose GD, Young WB. Interior turns in globular proteins. Nature 1983;304:655-657.
-
(1983)
Nature
, vol.304
, pp. 655-657
-
-
Rose, G.D.1
Young, W.B.2
-
5
-
-
0027082924
-
Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications
-
Meyer E. Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications. Prot Sci 1992;1:1543-1562.
-
(1992)
Prot Sci
, vol.1
, pp. 1543-1562
-
-
Meyer, E.1
-
6
-
-
0028095182
-
Buried waters and internal cavities in monomeric proteins
-
Williams MA, Goodfellow JM, Thornton JM. Buried waters and internal cavities in monomeric proteins. Prot Sci 1994;3:1224-1235.
-
(1994)
Prot Sci
, vol.3
, pp. 1224-1235
-
-
Williams, M.A.1
Goodfellow, J.M.2
Thornton, J.M.3
-
7
-
-
0035937261
-
Core and surface mutations a ect folding kinetics, stability, and cooperativity I IL-1b: Does alteration in buried water play a role?
-
Covalt JC, Roy M, Jennings PA. Core and surface mutations a ect folding kinetics, stability, and cooperativity I IL-1b: Does alteration in buried water play a role? J Mol Biol 2001;307:657-669.
-
(2001)
J Mol Biol
, vol.307
, pp. 657-669
-
-
Covalt, J.C.1
Roy, M.2
Jennings, P.A.3
-
8
-
-
0034024888
-
Structural water molecules in the family of fatty acid binding proteins
-
Likic VA, Juranic N, Macura S, Prendergast FG. Structural water molecules in the family of fatty acid binding proteins. Prot Sci 2000;9:497-504.
-
(2000)
Prot Sci
, vol.9
, pp. 497-504
-
-
Likic, V.A.1
Juranic, N.2
Macura, S.3
Prendergast, F.G.4
-
9
-
-
0027068111
-
Buried water in homologous serine proteases
-
Sreenivasan U, Axelsen PH. Buried water in homologous serine proteases. Biochemistry 1992;31:12785-12791.
-
(1992)
Biochemistry
, vol.31
, pp. 12785-12791
-
-
Sreenivasan, U.1
Axelsen, P.H.2
-
10
-
-
0027164289
-
Designed replacement of an internal hydration water molecule in BPTI: Structural and functional implications of a glycine-to-serine mutation
-
Berndt KD, Beunink J, Schroder W, Wüthrich K. Designed replacement of an internal hydration water molecule in BPTI: structural and functional implications of a glycine-to-serine mutation. Biochemistry 1993;32:4564-4570.
-
(1993)
Biochemistry
, vol.32
, pp. 4564-4570
-
-
Berndt, K.D.1
Beunink, J.2
Schroder, W.3
Wüthrich, K.4
-
11
-
-
0030696285
-
Contribution of water molecules in the interior of a protein to the conformational stability
-
Takano K, Funahashi J, Yamagata Y, Fujii S, Yutani K. Contribution of water molecules in the interior of a protein to the conformational stability. J Mol Biol 1997;274:132-142.
-
(1997)
J Mol Biol
, vol.274
, pp. 132-142
-
-
Takano, K.1
Funahashi, J.2
Yamagata, Y.3
Fujii, S.4
Yutani, K.5
-
12
-
-
0037154268
-
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after structural collapse
-
Cheung MS, García AE, Onuchic JN. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after structural collapse. Proc Natl Acad Sci USA 2002;99: 685-690.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 685-690
-
-
Cheung, M.S.1
García, A.E.2
Onuchic, J.N.3
-
13
-
-
1542297762
-
Solvation in protein folding analysis: Combination of theoretical and experimental approaches
-
Fernandez-Escamilla AM, Cheung MS, Vega MC, Wilmanns M, Onuchic JN, Serrano L. Solvation in protein folding analysis: combination of theoretical and experimental approaches. Proc Natl Acad Sci USA 2004;101:2834-2839.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 2834-2839
-
-
Fernandez-Escamilla, A.M.1
Cheung, M.S.2
Vega, M.C.3
Wilmanns, M.4
Onuchic, J.N.5
Serrano, L.6
-
16
-
-
0035859887
-
The active site dynamics of 4-chlorobenzoylcoa dehalogenase
-
Lau EY, Bruice TC. The active site dynamics of 4-chlorobenzoylcoa dehalogenase. Proc Natl Acad Sci USA 2001;98:9527-9532.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 9527-9532
-
-
Lau, E.Y.1
Bruice, T.C.2
-
17
-
-
0037941108
-
Static and dynamic water molecules in Cu, Zn superoxide dismutase
-
Falconi M, Brunelli M, Pesece A, Ferrario M, Bolognesi M, Desideri A. Static and dynamic water molecules in Cu, Zn superoxide dismutase. Proteins 2003;51:607-615.
-
(2003)
Proteins
, vol.51
, pp. 607-615
-
-
Falconi, M.1
Brunelli, M.2
Pesece, A.3
Ferrario, M.4
Bolognesi, M.5
Desideri, A.6
-
18
-
-
0030987236
-
Identification of a functional water channel in cytochrome p45-enzymes
-
Oprea TI, Hummer G, García AE. Identification of a functional water channel in cytochrome p45-enzymes. Proc Natl Acad Sci USA 1997;94:2133-2138.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 2133-2138
-
-
Oprea, T.I.1
Hummer, G.2
García, A.E.3
-
19
-
-
0031973948
-
Oxygen and proton pathways in cytochrome c oxidase
-
Hofacker I, Schulten K. Oxygen and proton pathways in cytochrome c oxidase. Proteins 1998;30:100-107.
-
(1998)
Proteins
, vol.30
, pp. 100-107
-
-
Hofacker, I.1
Schulten, K.2
-
20
-
-
0033609904
-
Structure of bacteriorhodopsin at 1.55 Å resolution
-
Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK. Structure of bacteriorhodopsin at 1.55 Å resolution. J Mol Biol 1999;291:899-911.
-
(1999)
J Mol Biol
, vol.291
, pp. 899-911
-
-
Luecke, H.1
Schobert, B.2
Richter, H.T.3
Cartailler, J.P.4
Lanyi, J.K.5
-
21
-
-
0028890031
-
Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans
-
Iwata S, Ostermeier C, Ludwig B, Michel H. Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 1995;376:660-669.
-
(1995)
Nature
, vol.376
, pp. 660-669
-
-
Iwata, S.1
Ostermeier, C.2
Ludwig, B.3
Michel, H.4
-
22
-
-
0034071764
-
Protein-bound water molecule counting by resolution of 1H spin-lattice relaxation mechanisms
-
Kühne S, Bryant RG. Protein-bound water molecule counting by resolution of 1H spin-lattice relaxation mechanisms. Biophys J 2000;78:2163-2169.
-
(2000)
Biophys J
, vol.78
, pp. 2163-2169
-
-
Kühne, S.1
Bryant, R.G.2
-
23
-
-
1842687872
-
Biomolecular cryocrystallography: Structural changes during flashcooling
-
Halle B. Biomolecular cryocrystallography: structural changes during flashcooling. Proc Natl Acad Sci USA 2004;101:4793-4798.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 4793-4798
-
-
Halle, B.1
-
24
-
-
0026326956
-
Protein hydration in aqueous solution
-
Otting G, Liepinsh E, Wuthrich K. Protein hydration in aqueous solution. Science 1991;254:974-980.
-
(1991)
Science
, vol.254
, pp. 974-980
-
-
Otting, G.1
Liepinsh, E.2
Wuthrich, K.3
-
25
-
-
0028948786
-
17O spin relaxation dispersion
-
17O spin relaxation dispersion. J Mol Biol 1995;245: 682-297.
-
(1995)
J Mol Biol
, vol.245
, pp. 682-1297
-
-
Denisov, V.P.1
Halle, B.2
-
26
-
-
0029081424
-
Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its g36s mutant
-
Denisov VP, Halle B, Peters J, Hörlein HD. Residence times of the buried water molecules in bovine pancreatic trypsin inhibitor and its g36s mutant. Biochemistry 1995;34:9046-9051.
-
(1995)
Biochemistry
, vol.34
, pp. 9046-9051
-
-
Denisov, V.P.1
Halle, B.2
Peters, J.3
Hörlein, H.D.4
-
28
-
-
0035902770
-
Microsecond exchange of internal water molecules in bacteriorhodopsin
-
Gottschalk M, Dencher NA, Halle B. Microsecond exchange of internal water molecules in bacteriorhodopsin. J Mol Biol 2001;311: 605-621.
-
(2001)
J Mol Biol
, vol.311
, pp. 605-621
-
-
Gottschalk, M.1
Dencher, N.A.2
Halle, B.3
-
29
-
-
0026189146
-
A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins
-
Wade RC, Mazor MH, McCammon JA, Quiocho FA. 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.C.1
Mazor, M.H.2
McCammon, J.A.3
Quiocho, F.A.4
-
30
-
-
0029160249
-
Thermodynamics of water mediating protein-ligand interactions in cytochrome p450cam: A molecular dynamics study
-
Helms V, Wade RC. Thermodynamics of water mediating protein-ligand interactions in cytochrome p450cam: a molecular dynamics study. Biophys J 1995;69:810-824.
-
(1995)
Biophys J
, vol.69
, pp. 810-824
-
-
Helms, V.1
Wade, R.C.2
-
31
-
-
0029126354
-
A comparison of neutron diffraction and molecular dynamics structures: Hydroxyl group and water molecule orientations in trypsin
-
McDowell RS, Kossiako AA. A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin. J Mol Biol 1995;250:553-570.
-
(1995)
J Mol Biol
, vol.250
, pp. 553-570
-
-
McDowell, R.S.1
Kossiako, A.A.2
-
32
-
-
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;71: 670-681.
-
(1996)
Biophys J
, vol.71
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Pomes, R.3
Smith, J.C.4
-
33
-
-
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
-
34
-
-
0034651984
-
Water penetration and escape in proteins
-
García AE, Hummer G. Water penetration and escape in proteins. Proteins 2000;38:261-272.
-
(2000)
Proteins
, vol.38
, pp. 261-272
-
-
García, A.E.1
Hummer, G.2
-
35
-
-
0033636839
-
Residence times of water molecules in the hydration sites of myoglobin
-
Makarov VA, Andrews BK, Smith PE, Pettit BM. Residence times of water molecules in the hydration sites of myoglobin. Biophys J 2000;79:2966-2974.
-
(2000)
Biophys J
, vol.79
, pp. 2966-2974
-
-
Makarov, V.A.1
Andrews, B.K.2
Smith, P.E.3
Pettit, B.M.4
-
36
-
-
0035314045
-
Dynamics of internal water in fatty acid binding protein: Computer simulations and comparison with experiments
-
Likic VA, Prendergast FG. Dynamics of internal water in fatty acid binding protein: computer simulations and comparison with experiments. Proteins 2001;43:65-72.
-
(2001)
Proteins
, vol.43
, pp. 65-72
-
-
Likic, V.A.1
Prendergast, F.G.2
-
37
-
-
0035940247
-
Dissecting the vibrational entropy changes on protein/ligand binding: Burial of a water molecule in bovine pancreatic trypsin inhibitor
-
Fischer S, Smith JC, Verma CS. Dissecting the vibrational entropy changes on protein/ligand binding: burial of a water molecule in bovine pancreatic trypsin inhibitor. 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
-
38
-
-
0035839052
-
Dynamics of hydration in hen egg white lysozyme
-
Sterpone F, Ceccarelli M, Marchi M. Dynamics of hydration in hen egg white lysozyme. J Mol Biol 2001;311:409-419.
-
(2001)
J Mol Biol
, vol.311
, pp. 409-419
-
-
Sterpone, F.1
Ceccarelli, M.2
Marchi, M.3
-
39
-
-
0037134267
-
Control of the selectivity of the aquaporin water channel family by global orientational tuning
-
Tajkhorshid E, Nollert P, Jensen MØ, Miercke LJW, O'Connell J, Stroud RM, Schulten K. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 2002;296:525-530.
-
(2002)
Science
, vol.296
, pp. 525-530
-
-
Tajkhorshid, E.1
Nollert, P.2
Jensen, M.Ø.3
Miercke, L.J.W.4
O'Connell, J.5
Stroud, R.M.6
Schulten, K.7
-
40
-
-
0036306105
-
Simulations of apo and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water
-
Bakowies D, van Gunsteren WF. Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. J Mol Biol 2002;315:713-736.
-
(2002)
J Mol Biol
, vol.315
, pp. 713-736
-
-
Bakowies, D.1
Van Gunsteren, W.F.2
-
41
-
-
2942659093
-
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method
-
Hamelberg D, McCammon JA. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc 2003;126:7683-7689.
-
(2003)
J Am Chem Soc
, vol.126
, pp. 7683-7689
-
-
Hamelberg, D.1
McCammon, J.A.2
-
42
-
-
1842534583
-
Mhc-peptide binding is assisted by bound water molecules
-
Petrone P, García 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.1
García, A.E.2
-
43
-
-
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
-
44
-
-
0025879501
-
In a staphylococcal nuclease mutant, the side-chain of a lysine replacing valine-66 is fully buried in the hydrophobic core
-
Stites WE, Gittis AG, Lattman EE, Shortle D. In a staphylococcal nuclease mutant, the side-chain of a lysine replacing valine-66 is fully buried in the hydrophobic core. J Mol Biol 1991;221:7-14.
-
(1991)
J Mol Biol
, vol.221
, pp. 7-14
-
-
Stites, W.E.1
Gittis, A.G.2
Lattman, E.E.3
Shortle, D.4
-
45
-
-
0040321024
-
Experimental measurement of the effective dielectric in the hydrophobic core of a protein
-
García-Moreno EB, Dwyer JJ, Gittis AG, Lattman EE, Spencer DS, Stites WE. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys Chem 1997;64: 211-224.
-
(1997)
Biophys Chem
, vol.64
, pp. 211-224
-
-
García-Moreno, E.B.1
Dwyer, J.J.2
Gittis, A.G.3
Lattman, E.E.4
Spencer, D.S.5
Stites, W.E.6
-
46
-
-
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, García-Moreno EB. High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys J 2000;79: 1610-1620.
-
(2000)
Biophys 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
García-Moreno, E.B.7
-
47
-
-
3342908886
-
X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: Insights into polarity of the protein interior
-
Nguyen DM, Reynald RL, Gittis AG, Lattman EE. X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior. J Mol Biol 2004;341:565-574.
-
(2004)
J Mol Biol
, vol.341
, pp. 565-574
-
-
Nguyen, D.M.1
Reynald, R.L.2
Gittis, A.G.3
Lattman, E.E.4
-
48
-
-
10044267947
-
Stabilization of internal charges in a protein: Water penetration or conformational change?
-
Denisov VP, Schlessman JL, García-Moreno EB, Halle B. Stabilization of internal charges in a protein: water penetration or conformational change? Biophys J 2004;87:3982-3994.
-
(2004)
Biophys J
, vol.87
, pp. 3982-3994
-
-
Denisov, V.P.1
Schlessman, J.L.2
García-Moreno, E.B.3
Halle, B.4
-
49
-
-
0036099192
-
Experimental pK(a) values of buried residues: Analysis with continuum methods and role of water penetration
-
Fitch CA, Karp DA, Lee KK, States WE, Lattman EE, García-Moreno EB. Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration. Biophys J 2002;82:3289-304.
-
(2002)
Biophys J
, vol.82
, pp. 3289-3304
-
-
Fitch, C.A.1
Karp, D.A.2
Lee, K.K.3
States, W.E.4
Lattman, E.E.5
García-Moreno, E.B.6
-
50
-
-
0035451052
-
What are the dielectric constants of proteins and how to validate electrostatic models?
-
Schutz CN, Warshel A. What are the dielectric constants of proteins and how to validate electrostatic models? Proteins 2002; 44:400-417.
-
(2002)
Proteins
, vol.44
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
51
-
-
0036228118
-
Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein
-
Lee KK, Fitch CA, García-Moreno EB. Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein. Protein Sci 2002;11:1004-1016.
-
(2002)
Protein Sci
, vol.11
, pp. 1004-1016
-
-
Lee, K.K.1
Fitch, C.A.2
García-Moreno, E.B.3
-
52
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K. NAMD2: greater scalability for parallel molecular dynamics. J Comp Phys 1999;151:283-312.
-
(1999)
J Comp Phys
, vol.151
, pp. 283-312
-
-
Kalé, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
54
-
-
0041784950
-
Allhydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field
-
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, 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 IWE, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. Allhydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. 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.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, I.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..
-
55
-
-
36449007836
-
Constant pressure molecular dynamics simulation-the Langevin piston method
-
Feller SE, Zhang YH, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation-the Langevin piston method. J Chem Phys 1995;103:4613-4621.
-
(1995)
J Chem Phys
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
56
-
-
0029633186
-
AMBER, a package of computerprograms for applying molecular mechanics, normal-mode analysis, moleculardynamics and free-energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P. AMBER, a package of computerprograms for applying molecular mechanics, normal-mode analysis, moleculardynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput Phys Commun 1995;91:1-41.
-
(1995)
Comput Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
57
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995;117: 5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz Jr., K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
58
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;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
-
59
-
-
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
-
60
-
-
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
-
61
-
-
0025877987
-
The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution
-
Hynes TR, Fox RO. The crystal structure of staphylococcal nuclease refined at 1.7 Å resolution. Proteins 1991;10:92-105.
-
(1991)
Proteins
, vol.10
, pp. 92-105
-
-
Hynes, T.R.1
Fox, R.O.2
-
62
-
-
0001520216
-
Computation of the mean residence time of water in the hydration shells of biomolecules
-
García AE, Stiller L. Computation of the mean residence time of water in the hydration shells of biomolecules. J Comp Chem 1993;14:1396-1406.
-
(1993)
J Comp Chem
, vol.14
, pp. 1396-1406
-
-
García, A.E.1
Stiller, L.2
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