Advances in biomolecular simulations: Methodology and recent applications

Quarterly Reviews of Biophysics

Volumn 36, Issue 3, 2003, Pages 257-306

  Norberg, Jan ^a   Nilsson, Lennart ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE; NUCLEIC ACID; PHOSPHOLIPID; PROTEIN;

ALGORITHM; AQUEOUS SOLUTION; BIOCHEMISTRY; COMPLEX FORMATION; COMPUTER; CONFORMATION; HIGH TEMPERATURE PROCEDURES; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; POLARIZATION; PRESSURE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; REVIEW; SIMULATION; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

EID: 1442328108     PISSN: 00335835     EISSN: None     Source Type: Journal    
DOI: 10.1017/S0033583503003895     Document Type: Review

References (376)

1. ADAMS, D. J. (1979). Computer simulation of ionic systems: the distorting effects of the boundary conditions. Chemical Physics Letters 62, 329-332.
2. ALDER, B. J. & WAINWRIGHT, T. E. (1957). Phase transition for a hard sphere system. Journal of Chemical Physics 27, 1208-1209.
3. ALLEN, M. P. & TILDESLEY, D. J. (1987). Computer Simulation of Liquids. New York: Oxford University Press.
4. ALONSO, D. O. V., ALM, E. & DAGGETT, V. (2000). Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping. Structure, Folding & Design 8, 101-110.
5. AMARA, P., FIELD, M. J., ALHAMBRA, C. & GAO, J. (2000). The generalized hybrid orbital method for combined quantum mechanical/molecular mechanical calculations: formulation and tests of the analytical derivatives. Theoretical Chemical Accounts 104, 336-343.
6. ANDERSEN, H. C. (1980). Molecular dynamics simulations at constant pressure and/or temperature. Journal of Chemical Physics 72, 8205-8212.
7. ANDERSEN, H. C. (1983). RATTLE: a 'velocity' version of the SHAKE algorithm for molecular dynamics calculations. Journal of Computational Physics 52, 24-34.
8. ANFINSEN, C. B. (1973). Principles that govern the folding of protein chains. Science 181, 223-230.
9. ANTES, I. & THIEL, W. (1999). Adjusted connection atoms for combined quantum mechanical and molecular mechanical methods. Journal of Physical Chemistry (A) 103, 9290-9295.
10. ÅQVIST, J. & LUZHKOV, V. (2000). Ion permeation mechanism of the potassium channel. Nature 404, 881-884.
11. ÅQVIST, J., LUZHKOV, V. B. & BRANDSDAL, B. O. (2002). Ligand binding affinities from MD simulations. Accounts of Chemical Research 35, 358-365.
12. AUFFINGER, P. & BEVERIDGE, D. L. (1995). A simple test for evaluating the truncation effects in simulations of systems involving charged groups. Chemical Physics Letters 234, 413-415.
13. AUFFINGER, P. & WESTHOF, E. (1998). Simulations of the molecular dynamics of nucleic acids. Current Opinion in Structural Biology 8, 227-236.
14. BALSERA, M., STEPANIANTS, S., IZRAILEV, S., OONO, Y. & SCHULTEN, K. (1997). Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophysical Journal 73, 1281-1287.
15. BANAVALI, N. K., IM, W. & ROUX, B. (2002). Electrostatic free energy calculations using the generalized solvent boundary potential method. Journal of Chemical Physics 117, 7381-7388.
16. BANBA, S. & BROOKS III, C. L. (2000). Free energy screening of small ligands binding to an artificial protein cavity. Journal of Chemical Physics 113, 3423-3433.
17. BANBA, S., GUO, Z. Y. & BROOKS III, C. L. (2000). Efficient sampling of ligand orientations and conformations in free energy calculations using the λ-dynamics method. Journal of Physical Chemistry (B) 104, 6903-6910.
18. BANKS, J. L., KAMINSKI, G. A., ZHOU, R., MAINZ, D. T., BERNE, B. J. & FRIESNER, R. A. (1999). Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model. Journal of Chemical Physics 110, 741-754.
19. BARTELS, C. (2000). Analyzing biased Monte Carlo and molecular dynamics simulations. Chemical Physics Letters 331, 446-454.
20. BASMA, M., SUNDARA, S., ÇALGAN, D., VERNALI, T. & WOODS, R. J. (2001). Solvated ensemble averaging in the calculation of partial atomic charges. Journal of Computational Chemistry 22, 1125-1137.
21. BATCHO, P. F., CASE, D. A. & SCHLICK, T. (2001). Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations. Journal of Chemical Physics 115, 4003-4018.
22. BAYLY, C. I., CIEPLAK, P., CORNELL, W. D. & KOLLMAN, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving charges - the RESP model. Journal of Physical Chemistry 97, 10269-10280.
23. BEACHY, M., CHASMAN, D., MURPHY, R., HALGREN, T. & FRIESNER, R. (1997). Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. Journal of the American Chemical Society 119, 5908-5920.
24. BERENDSEN, H. J. C. (1993). Electrostatic interactions. In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications, pp. 161-181. Leiden: ESCOM.
25. BERENDSEN, H. J. C. & HAYWARD, S. (2000). Collective protein dynamics in relation to function. Current Opinion in Structural Biology 10, 165-169.
26. BERENDSEN, H. J. C., POSTMA, J. P. M., VAN GUNSTEREN, W. F., DINOLA, A. & HAAK, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics 81, 3684-3690.
27. BERENDSEN, H. J. C. & TIELEMAN, D. P. (1998). Molecular dynamics: studies of lipid bilayers. In Encyclopedia of computational chemistry, John Wiley and Sons, Chichester, 1639-1650.
28. BERKOWITZ, M. & MCCAMMON, J. A. (1982). Molecular dynamics with stochastic boundary conditions. Chemical Physics Letters 90, 215-217.
29. BERNE, B. J. & STRAUB, J. E. (1997). Novel methods of sampling phase space in the simulation of biological systems. Current Opinion in Structural Biology 7, 181-189.
30. + channel. Nature 414, 73-77.
31. BERTRAND, H. O., PULLMAN, A., ZAKRZEWSKA, K., HARTMANN, B. & FERMANDJIAN, S. (1999). Determination of a set of parameters for the molecular modelling of phosphorothioate DNA. Theoretical Chemical Accounts 101, 269-273.
32. BEVERIDGE, D. L. & DICAPUA, F. M. (1989). Free energy via molecular simulation - applications to chemical and biomolecular systems. Annual Review of Biophysics and Biophysical Chemistry 18, 431-492.
33. BEVERIDGE, D. L. & MCCONNELL, K. J. (2000). Nucleic acids: theory and computer simulation, Y2K. Current Opinion in Structural Biology 10, 182-196.
34. BOCZKO, E. M. & BROOKS III, C. L. (1993). Constant-temperature free energy surfaces for physical and chemical processes. Journal of Physical Chemistry 97, 4509-4513.
35. BOCZKO, E. M. & BROOKS III, C. L. (1995). First principles calculation of the folding free energy of a three-helix bundle protein. Science 269, 393-396.
36. BOND, C. J., WONG, K.-B., CLARKE, J., FERSHT, A. R. & DAGGETT, V. (1997). Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Proceedings of the National Academy of Sciences USA 94, 13409-13413.
37. BONVIN, A. M. J. J., MARK, A. E. & VAN GUNSTEREN, W. F. (2000). The GROMOS96 benchmarks for molecular simulations. Computer Physics Communications 128, 550-557.
38. BORESCH, S. & STEINHAUSER, O. (1999). Rationalizing the effects of modified electrostatic interactions in computer simulations: the dielectric self-consistent field method. Journal of Chemical Physics 111, 8271-8274.
39. BORN, M. & VON KARMEN, T. (1912). Über Schwingungen in Raumgittern. Physikalische Zeitschrift 13, 297-309.
40. BOSCH, D., FOLOPPE, N., PASTOR, N., PARDO, L. & CAMPILLO, M. (2001). Calibrating nucleic acids torsional energetics in force-field: insight from model compounds. Journal of Molecular Structure: Theochem 537, 283-305.
41. BROOKS, B. R., BRUCCOLERI, R. E., OLAFSON, B. D., STATES, D. J., SWAMINATHAN, S. & KARPLUS, M. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 93, 2487-2502.
42. BROOKS III, C. L. (1998). Simulations of protein folding and unfolding. Current Opinion in Structural Biology 8, 222-226.
43. BROOKS III, C. L., BRÜNGER, A. T. & KARPLUS, M. (1985a). Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers 24, 843-865.
44. BROOKS III, C. L. & CASE, D. A. (1993). Simulations of peptide conformational dynamics and thermodynamics. Chemical Reviews 93, 2487-2502.
45. BROOKS III, C. L. & KARPLUS, M. (1983). Deformable stochastic boundaries in molecular dynamics. Journal of Chemical Physics 79, 6312-6325.
46. BROOKS III, C. L., PETTITT, B. M. & KARPLUS, M. (1985b). Structural and energetic effects of truncating long range interactions in ionic and polar fluids. Journal of Chemical Physics 83, 5897-5908.
47. BROOKS III, C. L., PETTITT, B. M. & KARPLUS, M. (1988). Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, vol. 71. Advances in Chemical Physics. New York: John Wiley & Sons.
48. BRÜNGER, A. T., BROOKS, C. L. & KARPLUS, M. (1985). Active site dynamics of ribonuclease. Proceedings of the National Academy of Sciences USA 82, 8458-8462.
49. BURSULAYA, B. D. & BROOKS III, C. L. (1999). Folding free energy surface of a three-stranded β-sheet protein. Journal of the American Chemical Society, 121, 9947-9951.
50. BURSULAYA, B. D. & BROOKS III, C. L. (2000). Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with Explicit and Implicit solvent models. Journal of Physical Chemistry (B) 104, 12378-12383.
51. CAFLISCH, A. & KARPLUS, M. (1994). Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proceedings of the National Academy of Sciences USA 91, 1746-1750.
52. CAFLISCH, A. & KARPLUS, M. (1995). Acid and thermal denaturation of barnase investigated by molecular dynamics simulations. Journal of Molecular Biology 252, 672-708.
53. CAFLISCH, A. & KARPLUS, M. (1999). Structural details of urea binding to barnase: a molecular dynamics analysis. Strucure: Folding and Design 7, 477-488.
54. ÇAǦIN, T. & PETTITT, B. M. (1991a). Grand molecular dynamics: a method for open systems. Molecular Simulations 6, 5-26.
55. ÇAǦIN, T. & PETTITT, B. M. (1991b). Molecular dynamics with a variable number of molecules. Molecular Physics 72, 169-175.
56. ÇAǦIN, T. & PETTITT, B. M. (1991c). A method for modeling icosahedral virions - rotational symmetry boundary-conditions. Journal of Computational Chemistry 12, 627-634.
57. CARLSON, H. A., MASUKAWA, K. M. & MCCAMMON, J. A. (1999). Method for including the dynamic fluctuations of a protein in computer-aided drug design. Journal of Physical Chemistry (A) 103, 10213-10219.
58. CHEATHAM III, T. E. & BROOKS, B. R. (1998). Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution. Theoretical Chemical Accounts 99, 279-288.
59. CHEATHAM III, T. E. & KOLLMAN, P. A. (2000). Molecular dynamics simulation of nucleic acids. Annual Review of Physical Chemistry 51, 435-471.
60. CHEN, X. & TROPSHA, A. (1999). Generalized linear response method: application to hydration free energy calculations. Journal of Computational Chemistry 20, 749-759.
61. CHENG, A., BEST, S. A., MERZ JR., K. M. & REYNOLDS, C. H. (2000). GB/SA water model for the Merck molecular force field (MMFF). Journal of Molecular Graphics and Modelling 18, 273-282.
62. CHENG, A. & MERZ JR., K. M. (1999). Application of a multiple time step algorithm to biomolecular systems. Journal of Physical Chemistry (B) 103, 5396-5405.
63. CHENG, H., GREENGARD, L. & ROKHLIN, V. (1999). A fast adaptive multipole algorithm in three dimensions. Journal of Computational Physics 155, 468-498.
64. CHRISTIANSON, L. A., LUCERO, M. J., APPELLA, D. H., KLEIN, D. A. & GELLMAN, S. H. (2000). Improved treatment of cyclic β-amino acids and successful prediction of β-peptide secondary structure using a modified force field: AMBER*C. Journal of Computational Chemistry 21, 763-773.
65. CHUN, H. M., PADILLA, C. E., CHIN, D. N., WATANABE, M., KARLOV, V. I., ALPER, H. E., SOOSAAR, K., BLAIR, K. B., BECKER, O. M., CAVES, L. S. D., NAGLE, R., HANEY, D. N. & FARMER, B. L. (2000). MBO(N)D: a multibody method for long-time molecular dynamics simulations. Journal of Computational Chemistry 21, 159-184.
66. CICCOTTI, G., MARTYNA, G. J., MELCHIONNA, S. & TUCKERMAN, M. E. (2001). Constrained isothermal-isobaric molecular dynamics with full atomic virial. Journal of Physical Chemistry (B) 105, 6710-6715.
67. CIEPLAK, P., CALDWELL, J. & KOLLMAN, P. (2001). Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. Journal of Computational Chemistry 22, 1048-1057.
68. CLARKE, J., HOUNSLOW, A. M., BOND, C. J., FERSHT, A. R. & DAGGETT, V. (2000). The effects of disulfide bonds on the denatured state of barnase. Protein Science 9, 2394-2404.
69. CORCHO, F. J., FILIZOLA, M. & PÉREZ, J. J. (2000). Evaluation of the iterative simulated annealing technique in conformational search of peptides. Chemical Physics Letters 319, 65-70.
70. CORNELL, W. D., CIEPLAK, P., BAYLY, C. I., GOULD, I. R., MERZ JR., K. M., FERGUSON, D. M., SPELLMEYER, D. C., FOX, T., CALDWELL, J. W. & KOLLMAN, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids and organic molecules. Journal of the American Chemical Society 117, 5179-5197.
71. CRAMER, C. J. & TRUHLAR, D. G. (1999). Implicit solvation models: equilibria, structure, spectra, and dynamics. Chemistry Reviews 99, 2161-2200.
72. CROUZY, S., BAUDRY, J., SMITH, J. C. & ROUX, B. (1999). Efficient calculation of two-dimensional adiabatic and free energy maps: application to the isomerization of the C13=C14 and C15=C16 bonds in the retinal of bacteriorhodopsin. Journal of Computational Chemistry 20, 1644-1658.
73. CUI Q., ELSTNER, M., KAXIRAS, E., FRAUENHEIM, T. & KARPLUS, M. (2001). A QM/MM implementation of the self-consistent charge density functional right binding (SCC-DFTB) method. Journal of Physical Chemistry (B) 105, 569-585.
74. CZERMINSKI, R. & ELBER, R. (1991). Computational studies of ligand diffusion in globins: I. Leghemoglobin. Proteins: Structure, Function and Genetics 10, 70-80.
75. DAGGETT, V. (2000). Long timescale simulations. Current Opinion in Structural Biology 10, 160-164.
76. DAGGETT, V. (2002). Molecular dynamics simulations of the protein unfolding/folding reaction. Accounts of Chemical Research 35, 422-429.
77. DAGGETT, V. & LEVITT, M. (1992). A model of the molten globule state from molecular dynamics simulations. Proceedings of the National Academy of Sciences USA 89, 5142-5146.
78. DAGGETT, V. & LEVITT, M. (1993). Protein unfolding pathways explored through molecular dynamics simulations. Journal of Molecular Biology 232, 600-619.
79. DAGGETT, V., LI, A. & FERSHT, A. R. (1998). Combined molecular dynamics and φ-value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: structural basis of Hammond and anti-Hammond effects. Journal of the American Chemical Society 120, 12740-12754.
80. DAMM, W. & VAN GUNSTEREN, W. F. (2000). Reversible peptide folding: dependence on molecular force field used. Journal of Computational Chemistry 21, 774-787.
81. DARDEN, T., PERERA, L., LI, L. & PEDERSEN, L. (1999). New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure, Folding & Design 7, R55-R60.
82. DARDEN, T. A., TOUKMAJI, A. & PEDERSEN, L. G. (1997). Long-range electrostatic effects in biomolecular simulations. Journal de Chimie Physique et de Physico-Chimie Biologique 94, 1346-1364.
83. DARDEN, T., YORK, D. & PEDERSEN, L. (1993). Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. Journal of Chemical Physics 98, 10089-10092.
84. DAURA, X., JAUN, B., SEEBACH, D., VAN GUNSTEREN, W. F. & MARK, A. E. (1998a). Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology 280, 925-932.
85. DAURA, X., MARK, A. E. & VAN GUNSTEREN, W. F. (1998b). Parametrization of aliphatic CHn united atoms of GROMOS96 force field. Journal of Computational Chemistry 19, 535-547.
86. DAURA, X., MARK, A. E. & VAN GUNSTEREN, W. F. (1999a). Peptide folding simulations: no solvent required? Computer Physics Communications 123, 97-102.
87. DAURA, X., VAN GUNSTEREN, W. F. & MARK, A. E. (1999b). Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins: Structure, Function and Genetics 34, 269-280.
88. DAURA, X., VAN GUNSTEREN, W. F., RIGO, D., JAUN, B. & SEEBACH, D. (1997). Studying the stability of a helical β-heptapeptide by molecular dynamics simulations. Chemistry: A European Journal 3, 1410-1417.
89. DE GROOT, B. L., VAN AALTEN, D. M. F., SCHEEK, R. M., AMADEI, A., VRIEND, G. & BERENDSEN, H. J. C. (1997). Prediction of protein conformational freedom from distance constraints. Proteins: Structure, Function and Genetics 29, 240-251.
90. DE GROOT, B. L. & GRUBMÜLLER, H. (2001). Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294, 2353-2357.
91. DESERNO, M. & HOLM, C. (1998a). How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. Journal of Chemical Physics 109, 7678-7693.
92. DESERNO, M. & HOLM, C. (1998b). How to mesh up Ewald sums. II. An accurate error estimate for the particle-particle-particle-mesh algorithm. Journal of Chemical Physics 109, 7694-7701.
93. DUAN, Y. & KOLLMAN, P. A. (1998). Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282, 740-744.
94. DUAN, Y., WANG, L. & KOLLMAN, P. A. (1998). The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proceedings of the National Academy of Sciences USA 95, 9897-9902.
95. DUAN, Z.-H. & KRASNY, R. (2000). An Ewald summation based multipole method. Journal of Chemical Physics 113, 3492-3495.
96. EGBERTS, E., MARRINK, S. J. & BERENDSEN, H. J. C. (1994). Molecular dynamics simulation of a phospholipid membrane. European Biophysics Journal 22, 423-436.
97. EGOROV, S. A., RABANI, E. & BERNE, B. J. (1999). On the adequacy of mixed quantum-classical dynamics in condensed phase systems. Journal of Physical Chemistry B 103, 10978-10991.
98. ESSMANN, U., PERERA, L., BERKOWITZ, M. L., DARDEN, T., LEE, H. & PEDERSEN, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics 103, 8577-8593.
99. EVANS, D. J. & MORRIS, G. P. (1983). Isothermal isobaric molecular dynamics. Chemical Physics 77, 63-66.
100. EVANS, D. J. & MORRIS, G. P. (1984). Non-Newtonian molecular dynamics. Computer Physics Reports 1, 297-344.
101. EVANS, E. & RITCHIE, K. (1997). Dynamic strength of molecular adhesion bonds. Biophysical Journal 72, 1541-1555.
102. EWALD, P. P. (1921). Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen der Physik 64, 253-287.
103. FEENSTRA, K. A., HESS, B. & BERENDSEN, H. J. C. (1999). Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. Journal of Computational Chemistry 20, 786-798.
104. FEIG, M., MACKERELL JR., A. D. & BROOKS III, C. L. (2003). Force field influence on the observation of π-helical protein structures in molecular dynamics simulations. Journal of Physical Chemistry (B) 107, 2831-2836.
105. FELLER, S. E. & MACKERELL JR., A. D. (2000). An improved empirical potential energy function for molecular simulations of phospholipids. Journal of Physical Chemistry (B) 104, 7510-7515.
106. FELLER, S. E., YIN, D., PASTOR, R. W. & MACKERELL JR., A. D. (1997). Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies. Biophysical Journal 73, 2269-2279.
107. FELLER, S. E., ZHANG, Y., PASTOR, R. W. & BROOKS, B. R. (1995). Constant pressure molecular dynamics simulation: the Langevin piston method. Journal of Chemical Physics 103, 4613-4621.
108. FERRARA, P., APOSTOLAKIS, J. & CAFLISCH, A. (2000). Targeted molecular dynamics simulations of protein unfolding. Journal of Physical Chemistry (B) 104, 4511-4518.
109. FERRARA, P. & CAFLISCH, A. (2000). Folding simulations of a three-stranded antiparallel β-sheet peptide. Proceedings of the National Academy of Sciences USA 97, 10780-10785.
110. FERRENBERG, A. M. & SWENDSEN, R. H. (1989). Optimized Monte Carlo data analysis. Physical Review Letters 63, 1195-1198.
111. FERSHT, A. R. (1995). Characterizing transition states in protein folding: an essential step in the puzzle. Current Opinion in Structural Biology 5, 79-84.
112. FIELD, M. J., ALBE, M., BRET, C., PROUST-DE MARTIN, F. & THOMAS, A. (2000). The Dynamo library for molecular simulations using hybrid quantum mechanical and molecular mechanical potentials. Journal of Computational Chemistry 21, 1088-1100.
113. FIELD, M. J., BASH, P. A. & KARPLUS, M. (1990). A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. Journal of Computational Chemistry 11, 700-733.
114. FIGUEIRIDO, F., LEVY, R. M., ZHOU, R. H. & BERNE, B. J. (1997). Large scale simulation of macromolecules in solution: combining the periodic fast multipole method with multiple time step integrators. Journal of Chemical Physics 106, 9835-9849. [Correction (1997), 107, 7002.]
115. FLORIANO, W. B., NASCIMENTO, M. A. C., DOMONT, G. B. & GODDARD III, W. A. (1998). Effects of pressure on the structure of metmyoglobin: molecular dynamics predictions for pressure unfolding through a molten globule intermediate. Protein Science 7, 2301-2313.
116. FOLOPPE, N. & MACKERELL, JR., A. D. (2000). All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. Journal of Computational Chemistry 21, 86-104.
117. FORESTER, T. R. & SMITH, W. (1998). SHAKE, rattle, and roll: efficient constraint algorithms for linked rigid bodies. Journal of Computational Chemistry 19, 102-111. [Erratum (2000), 21, 157.]
118. FORREST, D. K. & SANSOM, M. S. P. (2000). Membrane simulations: bigger and better? Current Opinion in Structural Biology 10, 174-181.
119. FULTON, K. F., MAIN, E. R. G., DAGGETT, V. & JACKSON, S. E. (1999). Mapping the interactions present in the transition state for unfolding/folding of FKBP12. Journal of Molecular Biology 291, 445-461.
120. GAO, J. L., AMARA, P., ALHAMBRA, C. & FIELD, M. J. (1998). A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations. Journal of Physical Chemistry (A) 102, 4714-4721.
121. GARCÍA-ARCHILLA, B., SANZ-SERNA, J. M. & SKEEL, R. D. (1998). In Numerical Analysis 1997 (eds. D. F. Griffiths & G. A. Watson), pp. 318-331. London: Pitman.
122. GILQUIN, B., GUILBERT, C. & PERAHIA, D. (2000). Unfolding of hen egg lysozyme by molecular dynamics simulations at 300 K: insight into the role of the interdomain interface. Proteins: Structure, Function and Genetics 41, 58-74.
123. GILSON, M. K., GIVEN, J. A., BUSH, B. L. & MCCAMMON, J. A. (1997). The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophysical Journal 72, 1047-1069.
124. GREENGARD, L. & ROKHLIN, V. (1987). A fast algorithm for particle simulations. Journal of Computational Physics 73, 325-348.
125. GRESH, N., GUO, H., SALAHUB, D. R., ROQUES, B. P. & KAFAFI, S. A. (1999). Critical role of anisotropy for the dimerization energies of two protein-protein recognition motifs: cis-N-methylacetamide versus a beta-sheet conformer of alanine dipeptide. A joint ab initio, density functional theory, and molecular mechanics investigation. Journal of the American Chemical Society 121, 7885-7894.
126. GROOTENHUIS, P. D. J. & HAASNOOT, C. A. G. (1993). A CHARMM based force-field for carbohydrates using the CHEAT approach - carbohydrate hydroxyl-groups represented by extended atoms. Molecular Simulation 10, 75-95.
127. GRUBMÜLLER, H. (1995). Predicting slow structural transitions in macromolecular systems - conformational flooding. Physical Review (E) 52, 2893-2906.
128. GRUBMÜLLER, H. & TAVAN, P. (1998). Multiple time step algorithms for molecular dynamics simulations of proteins: how good are they? Journal of Computational Chemistry 19, 1534-1552.
129. GUENOT, J. & KOLLMAN, P. A. (1992). Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor. Protein Science 1, 1185-1205.
130. GULLINGSRUD, J., BRAUN, R. & SCHULTEN, K. (1999). Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. Journal of Computational Physics 151, 190-212.
131. GUO, Z. Y., BROOKS III, C. L. & BOCZKO, E. M. (1997). Exploring the folding free energy surface of a three-helix bundle protein. Proceedings of the National Academy of Sciences USA 94, 10161-10166.
132. HALGREN, T. A. (1999). MMFF VII. Characterization of MMFF94, MMFF94s and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. Journal of Computational Chemistry 20, 730-748.
133. HALGREN, T. A. & DAMM, W. (2001). Polarizable force fields. Current Opinion in Structural Biology 11, 236-242.
134. HART, R. K., PAPPU, R. V. & PONDER, J. W. (2000). Exploring the similarities between potential smoothing and simulated annealing. Journal of Computational Chemistry 21, 531-552.
135. HARVEY, S. C. (1989). Treatment of electrostatic effects in macromolecular modeling. Proteins: Structure, Function and Genetics 5, 78-92.
136. HENCHMAN, R. H. & ESSEX, J. W. (1999a). Free energy of hydration using restrained electrostatic potential derived charges via free energy perturbations and linear response. Journal of Computational Chemistry 20, 499-510.
137. HENCHMAN, R. H. & ESSEX, J. W. (1999b). Generation of OPLS-like charges from molecular electrostatic potential using restraints. Journal of Computational Chemistry 20, 483-498.
138. HENDRIX, D. A. & JARZYNSKI, C. (2001). A 'fast-growth' method of computing free energy differences. Journal of Chemical Physics 114, 5974-5981.
139. HERNÁNDEZ, B., LUQUE, F. J. & OROZCO, M. (2000). Mixed QM/MM molecular electrostatic potential. Journal of Computer-Aided Molecular Design 14, 329-339.
140. HESS, B., BEKKER, H., BERENDSEN, H. J. C. & FRAAIJE, J. G. E. M. (1997). LINCS: a linear constraint solver for molecular interactions. Journal of Computational Chemistry 18, 1463-1472.
141. HOCKNEY, R. W. & EASTWOOD, J. W. (1981). Computer Simulation Using Particles. New York: McGraw-Hill.
142. HOOVER, W. G. (1985). Canonical dynamics: equilibrium phase-space distributions. Physical Reviews (A) 31, 1695-1697.
143. HUMMER, G. (2001). Fast-growth thermodynamic integration: error and efficiency analysis. Journal of Chemical Physics 114, 7330-7337.
144. 3M) method for computing electrostatic interactions in molecular simulations. Journal of Chemical Physics 113, 10464-10476.
145. HÜNENBERGER, P. H. & MCCAMMON, J. A. (1999). Ewald artifacts in computer simulations of ionic solvation and ion-ion interaction: a continuum electrostatics study. Journal of Chemical Physics 110, 1856-1872.
146. HÜNENBERGER, P. H., MARK, A. E. & VAN GUNSTEREN, W. F. (1995). Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins: Structure, Function and Genetics 21, 196-213.
147. IM, W., BERNÈCHE, S. & ROUX, B. (2001). Generalized solvent boundary potential for computer simulations. Journal of Chemical Physics 114, 2924-2937.
148. ISRALEWITZ, B., GAO, M. & SCHULTEN, K. (2001). Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural Biology 11, 224-230.
149. IZAGUIRRE, J. A., REICH, S. & SKEEL, R. D. (1999). Longer time steps for molecular dynamics. Journal of Chemical Physics 110, 9853-9864.
150. JARZYNSKI, C. (1997). Nonequilibrium equality for free energy differences. Physical Reviews Letters 78, 2690-2693.
151. JI, J., ÇAǦIN, T. & PETTITT, B. M. (1992). Dynamic simulations of water at constant chemical-potential. Journal of Chemical Physics 96, 1333-1342.
152. JORGENSEN, W. L., MAXWELL, D. S. & TIRADO-RIVES, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society 118, 11225-11236.
153. JUFFER, A. H. & BERENDSEN, H. J. C. (1993). Dynamic surface boundary conditions. A simple boundary model for molecular dynamics simulations. Molecular Physics 79, 623-644.
154. KAMINSKI, G. A., FRIESNER, R. A., TIRADO-RIVES, J. & JORGENSEN, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via coparison with accurte quantum chemical calculations on peptides. Journal of Physical Chemistry (B) 105, 6474-6487.
155. KAMIYA, N. & HIGO, J. (2001). Repeated-annealing sampling combined with multicanonical algorithm for conformational sampling of bio-molecules. Journal of Computational Chemistry 22, 1098-1106.
156. KARPLUS, M. (2000). Aspects of protein reaction dynamics: deviations from simple behavior. Journal of Physical Chemistry (B) 104, 11-27.
157. KARPLUS, M. (2003). Molecular dynamics of biological macromolecules: a brief history and perspective. Biopolymers 68, 350-358.
158. KARPLUS, M. & MCCAMMON, J.A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology 9, 646-652.
159. KARPLUS, M. & PETSKO, G. A. (1990). Molecular-dynamics simulations in biology. Nature 347, 631-639.
160. KAWATA, M. & MIKAIMI, M. (1999). Acceleration of the canonical molecular dynamics by the particle mesh Ewald method combined with the multiple time-step integrator algorithm. Chemical Physics Letters 313, 261-266. [Corrigendum (2000), 317, 515.]
161. KAWATA, M. & MIKAMI, M. (2000). Computationally efficient canonical molecular dynamics simulations by using a multiple time-step integrator algorithm combined with the particle mesh Ewald method and with the fast multipole method. Journal of Computational Chemistry 21, 201-217.
162. KAWATA, M. & NAGASHIMA, U. (2001). Particle mesh Ewald method for three-dimensional systems with two-dimensional periodicity. Chemical Physics Letters 340, 165-172.
163. KAZMIRSKI, S. & DAGGETT, V. (1998a). The structural and dynamic properties of unfolded proteins: simulations of the 'molten coil' state of BPTI. Journal of Molecular Biology 277, 487-506.
164. KAZMIRSKI, S. & DAGGETT, V. (1998b). Non-native interactions in protein folding intermediates: molecular dynamics simulation of hen lysozyme. Journal of Molecular Biology, 284, 793-806.
165. KAZMIRSKI, S. L., LI, A. & DAGGETT, V. (1999). Analysis methods for comparison of nuclear dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. Journal of Molecular Biology 290, 283-304.
166. KIMURA, S. R., BROWER, R. C., ZHANG, C. & SUGIMORI, M. (2000). Surface of active polarons: a semiexplicit solvation method for biomolecular dynamics. Journal of Chemical Physics 112, 7723-7734.
167. KING, G. & BARFORD, R. A. (1993). Calculation of electrostatic free-energy differences with a time-saving approximate method. Journal of Physical Chemistry 97, 8798-8802.
168. KLAMT, A. & SCHÜÜRMANN, G. (1993). Cosmo - a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. Journal of the Chemical Society - Perkin Transactions (2) 5, 799-805.
169. KLEINJUNG, J., BAYLEY, P. & FRATERNALI, F. (2000). Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution. FEBS Letters 470, 257-262.
170. KNELLER, G.R. & MÜLDERS, T. (1996). Nosé-Andersen dynamics of partially rigid molecules: coupling all degrees of freedom to heat and pressure baths. Physical Reviews (E) 54, 6825-6837.
171. KOLB, A. & DÜNWEG, B. (1999). Optimized constant pressure stochastic dynamics. Journal of Chemical Physics 111, 4453-4459.
172. KOLLMAN, P. A. (1993). Free energy calculations: applications to chemical and biochemical phenomena. Chemical Reviews 93, 2395-2417.
173. KOLLMAN, P. A. (1996). Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Accounts of Chemical Research 29, 461-469.
174. KOLLMAN, P.A., KUHN, B., DONINI, O., PERÄKYLÄ, M., STANTON, R. & BAKOWIES, D. (2001). Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and aqueous solution. Accounts of Chemical Research 34, 72-79.
175. KOLLMAN, P. A., MASSOVA, I., REYES, C., KUHN, B., HUO, S., CHONG, L., LEE, M., LEE, T., DUAN, Y., WANG, W., DONINI, O., CIEPLAK, P., SRINIVASAN, J., CASE, D. A. & CHEATHAM III, T. E. (2000). Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research 33, 889-897.
176. KONG, X. J. & BROOKS III, C. L. (1996). γ-dynamics: a new approach to free energy calculations. Journal of Chemical Physics 105, 2414-2423.
177. KOUWIJZER, M. L. C. E. & GROOTENHUIS, P. D. J. (1995). Parametrization and application of CHEAT95, an extended atom force field for hydrated (oligo)saccharides. Journal of Physical Chemistry 99, 13426-13436.
178. KRATKY, K. W. (1980). New boundary condition for computer experiments of thermodynamic systems. Journal of Computational Physics 37, 205-217.
179. KRÄUTLER, V., VAN GUNSTEREN, W. F. & HÜNENBERGER, P. H. (2001). A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of Computational Chemistry 22, 501-508.
180. KUMAR, S., BOUZIDA, D., SWENDSEN, R. H., KOLLMAN, P. A. & ROSENBERG, J.M. (1992). The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method. Journal of Computational Chemistry 13, 1011-1021.
181. KUTEH, R. (1999). New methods for incorporating nonholonomic constraints into molecular dynamics simulations. Journal of Chemical Physics 111, 1394-1409.
182. LABERGE, L. J. & TULLY, J. C. (2000). A rigorous procedure for combining molecular dynamics and Monte Carlo simulation algorithms. Chemical Physics 260, 183-191.
183. LADURNER, A. G., ITZHAKI, L. S., DAGGET, V. & FERSHT, A.R. (1998). Synergy between simulation and experiment in describing the energy landscape of protein folding. Proceedings of the National Academy of Sciences USA 95, 8473-8478.
184. LAHIRI, A., NILSSON, L. & LAAKSONEN, A. (2001). Exploring the Idea of self-guided dynamics. Journal of Chemical Physics 114, 5993-5999.
185. LAMB, M. L. & JORGENSEN, W. L. (1997). Computational approaches to molecular recognition. Current Opinion in Chemical Biology 1, 449-457.
186. LANGLEY, D. R. (1998). Molecular dynamics simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results. Journal of Biomolecular and Structural Dynamics 16, 487-509.
187. LAVERY, R., ZAKREWSKA, K. & SKLENAR, H. (1995). JUMNA (JUnction Minimization of Nucleic-Acids). Computer Physics Communications 91, 135-158.
188. LAZARIDIS, T. & KARPLUS, M. (1997). New view of protein folding reconciled with the old through multiple unfolding simulations. Science 278, 1928-1931.
189. LAZARIDIS, T. & KARPLUS, M. (1999). Effective energy function for proteins in solution. Proteins: Structure, Function and Genetics 35, 133-152.
190. LAZARIDIS, T. & KARPLUS, M. (2000). Effective energy functions for protein structure prediction. Current Opinion in Structural Biology 10, 139-145.
191. LAZARIDIS, T. & KARPLUS, M. (2003). Thermodynamics of protein folding: a microscopic view. Biophysical Chemistry 100, 367-395.
192. LEDAUPHIN, V. & VERGOTEN, G. (2000). New nonbonded interactions calculation strategy for rectangular systems. I. Preliminary molecular dynamics study of solvated Na ion. Biopolymers 57, 373-382.
193. LEE, J., PILLARDY, J., CZAPLEWSKI, C., ARNAUTOVA, Y., RIPOLL, D. R., LIWO, A., GIBSON, K. D., WAWAK, R. J. & SCHERAGA, H. A. (2000a). Efficient parallel algorithms in global optimization of potential energy functions for peptides, proteins, and crystals. Computer Physics Communications 128, 399-411.
194. LEE, M. R., DUAN, Y. & KOLLMAN, P. A. (2000b). Use of MM/PB-SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins: Structure, Function and Genetics 39, 309-316.
195. LEE, S.-H., PALMO, K. & KRIMM, S. (2001). A new formalism for molecular dynamics in internal coordinates. Chemical Physics 265, 63-85.
196. LEIMKUHLER, B. & REICH, S. (2001). A reversible averaging integrator for multiple time-scale dynamics. Journal of Computational Physics 171, 95-114.
197. LEVITT, M. (1983). Computer simulation of DNA double-helix dynamics. Cold Spring Harbor Symposium on Quantative Biology, 47, 251-262.
198. LEVITT, M. (2001). The birth of computational structural biology. Nature Structural Biology 8, 392-393.
199. LEVITT, M., HIRSHBERG, M., SHARON, R. & DAGGETT, V. (1995). Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Computer Physics Communications 91, 215-231.
200. LÉVY, B. & ENESCU, M. (1998). Theoretical study of methylene blue: a new method to determine partial atomic charges; investigation of the interaction with guanine. Journal of Molecular Structure: Theochem 432, 235-245.
201. LEVY, R. M. & GALLICCHIO, E. (1998). Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects. Annual Review of Physical Chemistry 49, 531-567.
202. LI, A. & DAGGEETT, V. (1994). Charaterization of the transition state of protein unfolding: chymotrypsin inhibitor 2. Proceedings of the National Academy of Sciences USA 91, 10430-10434.
203. LI, A. & DAGGETT, V. (1996). Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. Journal of Molecular Biology 257, 412-429.
204. LI, A. & DAGGETT, V. (1998). The unfolding of barnase: charaterization of the major intermediate. Journal of Molecular Biology 275, 677-694.
205. LIU, H., MARK, A. E. & VAN GUNSTEREN, W. F. (1996). Estimating the relative free energy of different states with respect to a single reference state. Journal of Physical Chemistry 100, 9485-9494.
206. 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.
207. LU, H., KRAMMER, A., ISRALEWITZ, B., VOGEL, V. & SCHULTEN, K. (2000). Computer modeling of force-induced titin domain unfolding. Advances in Experimental and Medical Biology 481, 143-160.
208. LU, H. & SCHULTEN, K. (1999a). Steered molecular dynamics simulations of conformational changes of immunoglobulin domain I27 interpret atomic force microscopy observations. Chemical Physics 247, 141-153.
209. LU, H. & SCHULTEN, K. (1999b). Steered molecular dynamics simulations of force-induced protein domain unfolding. Proteins: Structure, Function and Genetics 35, 453-463.
210. LU, H. & SCHULTEN, K. (2000). The key event in force-induced unfolding of titin's immunoglobulin domains. Biophysical Journal 79, 51-65.
211. LU, N. & KOFKE, D. A. (2001). Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling. Journal of Chemical Physics 114, 7303-7311.
212. LÜDEMANN, S. K., LOUNNAS, V. & WADE, R. C. (2000). How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms. Journal of Molecular Biology 303, 797-811.
213. MA, J. & KARPLUS, M. (1997). Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proceedings of the National Academy of Sciences USA 94, 11905-11910.
214. MA, J., SIGLER, P. B., Xu, Z. & KARPLUS, M. (2000). A dynamic model for the allosteric mechanism of GroEL. Journal of Molecular Biology 302, 303-313.
215. MACKERELL JR., A. D. & BANAVALI, N. K. (2000). All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. Journal of Computational Chemistry 21, 105-120.
216. MACKERELL JR., A. D., BASHFORD, D., BELLOTT, M., DUNBRACK JR., R. L., EVANSECK, J. D., FIELD, M. J., FISCHER, S., GAO, J., GUO, H., HA, S., JOSEPH-MCCARTHY, D., KUCHNIR, L., KUCZERA, K., LAU, F. T. K., MATTOS, C., MICHNICK, S., NGO, T., NGUYEN, D.T., PRODHOM, B., REIHER III, W. E., ROUX, B., SCHLENKRICH, M., SMITH, J. C., STOTE, R., STRAUB, J., WATANABE, M., WÍRKIEWICZ-KUCZERA, J., YIN, D. & KARPLUS, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Phyical Chemistry (B) 102, 3586-3616.
217. MACKERELL. JR., A. D., WÍRKIEWICZ-KUCZERA, J. & KARPLUS, M. (1995). An all-atom empirical energy function for the simulation of nucleic acids. Journal of the American Chemical Society 117, 11946-11975.
218. MALEVANETS, A. & KAPRAL, R. (2000). Solute molecular dynamics in a mesoscale solvent. Journal of Chemical Physics 112, 7260-7269.
219. MANNFORS, B., PALMO, K. & KRIMM, S. (2000). A new electrostatic model for molecular mechanics force fields. Journal of Molecular Structure 556, 1-21.
220. MARCHI, M., BORGIS, D. & LEVY, N. (2001). A dielectric continuum molecular dynamics method. Journal of Chemical Physics 114, 4377-4385.
221. MARCHI, M. & PROCACCI, P. (1998). Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble. Journal of Chemical Physics 109, 5194-5202.
222. MARK, A. E. & VAN GUNSTEREN, W. F. (1992). Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state. Biochemistry 31, 7745-7748.
223. MARSZALEK, P. E., LU, H., LI, H., CARRION-VAZQUEZ, M., OBERHAUSER, A. F., SCHULTEN, K. & FERNANDEZ, J. M. (1999). Mechanical unfolding intermediates in titin modules. Nature 402, 100-103.
224. MARTÍ-RENOM, M. A., STOTE, R. H., QUEROL, E., AVILÉS, F. X. & KARPLUS, M. (1998). Refolding of potato carboxypeptidase inhibitor by molecular dynamics simulations with disulfide bond constraints. Journal of Molecular Biology 284, 145-172.
225. MARTYNA, G. J., KLEIN, M. L. & TUCKERMAN, M. (1992). Nosé-Hoover chains: the canonical ensemble via continuous dynamics. Journal of Chemical Physics 97, 2635-2643.
226. MARTYNA, G. J., TOBIAS, D. J. & KLEIN, M. L. (1994). Constant pressure molecular dynamics algorithms. Journal of Chemical Physics 101, 4177-4189.
227. MAYOR, U., JOHNSON, C. M., DAGGETT, V. & FERSHT, A. R. (2000). Protein folding and unfolding in microseconds to nanoseconds by experiments and simulations. Proceedings of the National Academy of Sciences USA 97, 13518-13522.
228. MCCAMMON, J.A. (1977). Molecular dynamics study of the bovine pancreatic trypsin inhibitor. In Models for Protein Dynamics 1976 (ed. H.J.C. Berendsen), pp. 137-152. Orsay, France: CECAM, Université de Paris IX.
229. MCCAMMON, J. A., GELIN, B. R. & KARPLUS, M. (1977). Dynamics of folded proteins. Nature 267, 585-590.
230. MCCAMMON, J. A. & HARVEY, S. C. (1987). Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
231. MELCHIONNA, S., CICCOTTI, G. & HOLIAN, B. L. (1993). Hoover NPT dynamics for systems varying in shape and size. Molecular Physics 78, 533-544.
232. MERTZ, J. E., TOBIAS, D. J., BROOKS, C. L. & SINGH, U. C. (1991). Vector and parallel algorithms for the molecular-dynamics simulation of macromolecules on shared memory computers. Journal of Computational Chemistry 12, 1270-1277.
233. MEZEI, M. (2000). Comment on 'Molecular dynamics simulations in the grand canonical ensemble: formulation of a bias potential for umbrella sampling'. Journal of Chemical Physics 112, 1059-1060.
234. MIRANKER, A. & KARPLUS, M. (1991). Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins: Structure, Function and Genetics 11, 29-34.
235. MIYAMOTO, S. & KOLLMAN, P. A. (1992). SETTLE - an analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry 13, 952-962.
236. MÖLLHOFF, M. & STERNBERG, U. (2001). Molecular mechanics with fluctuating atomic charges - a new force field with a semi-empirical charge calculation. Journal of Molecular Modelling 7, 90-102.
237. MONARD, G. & MERZ JR., K. M. (1999). Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Accounts of Chemical Research 32, 904-911.
238. MORDASINI, T. Z. & MCCAMMON, J. A. (2000). Calculations of relative hydration free energies: a comparative study using thermodynamic integration and an extrapolation method based on a single reference state. Journal of Physical Chemistry (8) 104, 360-367.
239. MORISHITA, T. (2000). Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath. Journal of Chemical Physics 113, 2976-2982.
240. NELSON, M., HUMPHREY, A., GURSOY, A., DALKE, A., KALE, R. D., SKEEL, R. D. & SCHULTEN, K. (1996). NAMD - a parallel, object-oriented molecular dynamics program. International Journal of Supercomputing Applications and High Performance Computing 10, 251-268.
241. NÉMETHY, G., GIBSON, K. D., PALMER, K. A., YOON, C. N., PATERLINI, G., ZAGARI, A., RUMSEY, S. & SHERAGA, H. A. (1992). Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. Journal of Physical Chemistry, 96, 6472-6484.
242. NORBERG, J. & NILSSON, L. (1995a). A conformational free energy landscape of ApApA from molecular dynamics simulations. Journal of Physical Chemistry 100, 2550-2554.
243. NORBERG, J. & NILSSON, L. (1995b). NMR relaxation times, dynamics, and hydration of a nucleic acid fragment from molecular dynamics simulations. Journal of Physical Chemistry 99, 14876-14884.
244. NORBERG, J. & NILSSON, L. (1996). Glass transition in DNA from molecular dynamics simulations. Proceedings of the National Academy of Sciences USA 93, 10173-10176.
245. NORBERG, J. & NILSSON, L. (2000). On the truncation of long-range electrostatic interactions in DNA. Biophysical Journal 79, 1537-1553.
246. NORBERG, J. & NILSSON, L. (2002). Molecular dynamics applied to nucleic acids. Accounts of Chemical Research 35, 465-472.
247. NOSÉ, S. & KLEIN, M. L. (1983). Constant pressure molecular dynamics for molecular systems. Molecular Physics 50, 1055-1076.
248. OKUYAMA-YOSHIDA, N., NAGAOKA, M. & YAMABE, T. (1998). Transition-state optimization on free energy surface: toward solution chemical reaction ergodography. International Journal of Quantum Chemistry 70, 95-103.
249. OKUYAMA-YOSHIDA, N., KATAOKA, K., NAGAOKA, M. & YAMABE, T. (2000). Structure optimization via free energy gradient method: application to glycine zwitterion in aqueous solution. Journal of Chemical Physics 113, 3519-3524.
250. OLIVA, B., DAURA, X., QUEROL, E. & AVILÉS, F. X. (2000). A generalized Langevin dynamics approach to model solvent dynamics effects on proteins via a solvent-accessible surface. The carboxypeptidase A inhibitor protein as a model. Theoretical Chemical Accounts 105, 101-109.
251. ONO, S., NAKAJIMA, N., HIGO, J. & NAKAMURA, H. (1999). The multicanonical weighted histogram analysis method for the free-energy landscape along structural transition paths. Chemical Physics Letters 12, 247-254.
252. ONO, S., NAKAJIMA, N., HIGO, J. & NAKAMURA, H. (2000). Peptide free-energy profile is strongly dependent on the force field: comparison of C96 and AMBER95. Journal of Computational Chemistry 21, 748-762.
253. ONUCHIC, J. N., LUTHEY-SCHULTEN, Z. & WOLYNES, P. G. (1997). Theory of protein folding: the energy landscape perspective. Annuual Review of Physical Chemistry, 48, 545-600.
254. OROZCO, M. & LUQUE, F.J. (2000). Theoretical methods for the description of the solvent effect in biomolecular systems. Chemical Reviews 100, 4187-4225. [Corrections (2001). 101, 203.]
255. OTA, N. & BRüNGER, A. T. (1997). Overcoming barriers in macromolecular simulations: non-Boltzmann thermodynamic integration. Theoretical Chemical Accounts 98, 171-181.
256. OTA, N., STROUPE, C., FERREIRA-DA-SILVA, J.M.S., SHAH, S. A., MARES-GUIA, M. & BRÜNGER, A. T. (1999). Non-Boltzmann thermodynamic integration ((NBTI) for macromolecular systems: relative free energy of binding of trypsin to benzamidine and benzylamine. Proteins: Structure, Function and Genetics 37, 641-653.
257. OTT, K.-H. & MEYER, B. (1996). Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations. Journal of Computational Chemistry 17, 1068-1084.
258. PACI, E. & KARPLUS, M. (1999). Forced unfolding of Fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. Journal of Molecular Biology, 288, 441-459.
259. PACI, E. & KARPLUS, M. (2000). Unfolding proteins by external forces and temperature: the importance of topology and energetics. Proceedings of the National Academy of Sciences USA 97, 6521-6526.
260. PAPPU, R. V., HART, R. K. & PONDER, J. W. (1998). Analysis and application of potential energy smoothing and search methods for global optimization. Journal of Physical Chemistry (B) 102, 9725-9742.
261. PEARLMAN, D. A., CASE, D. A., CALDWELL, J. W., ROSS, W.S., CHEATHAM III, T. E., DEBOLT, S., FERGUSON, D., SEIBEL, G. & KOLLMAN, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications 91, 1-41.
262. PÉREZ, S., IMBERTY, A., ENGELSEN, S. B., GRUZA, J., MAZEAU, K., JIMENEZ-BARBERO, J., POVEDA, A., ESPINOSA, J.-F., VAN EYCK, B. P., JOHNSON, G., FRENCH, A.D., KOUWIJZER, M. L. C. E., GROOTENUIS, P. D. J., BERNARDI, A., RAIMONDI, L., SENDEROWITZ, H., DURIER, V., VERGOTEN, G. & RASMUSSEN, K. (1998). A comparison and chemometric analysis of several molecular mechanics force fields and parameter sets applied to carbohydrates. Carbohydrate Research 314, 141-155.
263. PETTITT, B. M., MAKAROV, V. A. & ANDREWS, B. K. (1998). Protein hydration density: theory, simulations and crystallography. Current Opinion in Structural Biology 8, 218-221.
264. PHELPS, D. K., SPEELMAN, B. & POST, C. B. (2000). Theoretical studies of viral capsid proteins. Current Opinion in Structural Biology 10, 170-173.
265. PHILLIPS, S. C., ESSEX, J. W. & EDGE, C. M. (2000). Digitally filtered molecular dynamics: the frequency specific control of molecular dynamics simulations. Journal of Chemical Physics 112, 2586-2597.
266. POMÉS, R., EISENMESSER, E., POST, C. B. & ROUX, B. (1999). Calculating excess chemical potentials using dynamic simulations in the fourth dimension. Journal of Chemical Physics 111, 3387-3395.
267. 3M, FMM, and the Ewald method for large periodic Coulombic systems. Computer Physics Communications 95, 93-110.
268. PROCACCI, P. & BERNE, B.J. (1994). Multiple time scale methods for constant-pressure molecular dynamics simulations of molecular systems. Molecular Physics 83, 255-272.
269. RADMER, R. J. & KOLLMANN, P. A. (1997). Free energy calculation methods: a theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes. Journal of Computational Chemistry, 18, 902-919.
270. RAHMAN, A. (1964). Correlations in the motion of atoms in liquid argon. Physical Reviews 136A, 405-411.
271. RAHMAN, A. & STILLINGER, F. H. (1971). Molecular dynamics study of liquid water. Journal of Chemical Physics 55, 3336-3359.
272. REUTER, N., DEJAEGERE, A., MAIGRET, B. & KARPLUS, M. (2000). Frontier bonds in QM/MM methods: a comparison of different approaches. Journal of Physical Chemistry (A) 104, 1720-1735.
273. RICK, S. W., STUART, S. J. & BERNE, B. J. (1994). Dynamical fluctuating charge force-fields - application to liquid water. Journal of Chemical Physics 101, 6141-6156.
274. RIDARD, J. & LÉVY, B. (1999). Effective atomic charges in alanine dipeptide. Journal of Computational Chemistry 20, 473-482.
275. RIZZO, R. C. & JORGENSEN, W. L. (1999). OPLS all-atom model for amines: resolution of the amine hydration problem. Journal of the American Chemical Society 121, 4827-4836.
276. ROUX, B. & SIMONSON, T. (1999). Implicit solvent models. Biophysical Chemistry 78, 1-20.
277. ROZANSKA, X. & CHIPOT, C. (2000). Modeling ion-ion interaction in proteins: a molecular dynamics free energy calculation of the guanidinium-acetate association. Journal of Chemical Physics 112, 9691-9694.
278. RYCKAERT, J. P., ARIALDI, G. & MELCHIONNA, S. (2001). Molecular dynamics of polymers with explicit but frozen hydrogens. Molecular Physics 99, 155-165.
279. RYCKAERT, J. P., CICCOTTI, G. & BERENDSEN, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. Journal of Computational Physics 23, 327-341.
280. SAGUI, C. & DARDEN, T. A. (1999). Molecular dynamics simulations of biomolecules: long-range electrostatic effects. Annual Review of Biophysical and Biomolecular Structures 28, 155-179.
281. SAKANE, S., YEZDIMER, E. M., LIU, W., BARRIOCANAL, J. A., DOREN, D. J. & WOOD, R. H. (2000). Exploring the ab initio/classical free energy perturbation method: the hydration free energy of water. Journal of Chemical Physics 113, 2583-2593.
282. SANKARARAMAKRISHNAN, R., KONVICKA, K., MEHLER, E. L. & WEINSTEIN, H. (2000). Solvation in simulated annealing and high-temperature molecular dynamics of proteins: a restrained water droplet model. International Journal of Quantum Chemistry 77, 174-186.
283. SCHÄFER, H., VAN GUNSTEREN, W. F. & MARK, A. E. (1999). Estimating relative free energies from a single ensemble: hydration free energies. Journal of Computational Chemistry 20, 1604-1617.
284. SCHLENKRICH, M., BRINKMANN, J., MACKERELL JR., A. D. & KARPLUS, M. (1996). An empirical potential energy function for phospholipids: criteria for parameter optimization and applications. In Biological Membranes: A Molecular Perspective from Computation and Experiment (eds. K. M. Merz & B. Roux), pp. 31-81. Boston: Birkhäuser.
285. SCHLICK, T. (1999). Computational molecular biophysics today: a confluence of methodological advances and complex biomolecular applications. Journal of Computational Physics 151, 1-8.
286. SCHLICK, T., BARTH, E. & MANDZIUK, M. (1997). Biomolecular dynamics at long timesteps: bridging the time scale gap between simulation and experimentation. Annual Review of Biophysical and Biomolecular Structures 26, 181-222.
287. SCHLICK, T., SKEEL, R. D., BRUNGER, A.T., KALÉ, L. V., BOARD JR., J. A., HERMANS, J. & SCHULTEN, K. (1999). Algorithmic challenges in computational molecular biophysics. Journal of Computational Physics 151, 9-48.
288. SCHLITTER, J., ENGELS, M., KRUGER, P., JACOBY, E. & WOLLMER, A. (1993). Targeted molecular dynamics simulation of conformational change - application to the T→R transition in insulin. Molecular Simulation 10, 291-308.
289. SCHULER, L. D., DAURA, X. & VAN GUNSTEREN, W. F. (2001). An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. Journal of Computational Chemistry, 22, 1205-1218.
290. SCHYMKOWITZ, J. W. H., ROUSSEAU, F., IRVINE, L. R. & ITZHAKI, L. S. (2000). The folding pathway of the cell-cycle regulatory protein p13suc1: clues for the mechanism of domain swapping. Structure, Folding & Design 8, 89-100.
291. SCOTT, W. R. P., HÜNENBERG, P. H., TIRONI, I. G., MARK, A. E., BILLETER, S. R., FENNEN, J., TORDA, A. E., HUBER, T., KRÜGER, P. & VAN GUNSTEREN, W. F. (1999). The GROMOS biomolecular simulation program package. Journal of Physical Chemistry (A) 103, 3596-3607.
292. SEN, S. & NILSSON, L. (1999a). Some practical aspects of free energy calculations from molecular dynamics simulations. Journal of Computational Chemistry 20, 877-885.
293. SEN, S. & NILSSON, L. (1999b). Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation. Biophysical Journal 77, 1782-800.
294. SESSIONS, R. B., DAUBER-OSGUTHORPE, P. & OSGUTHORPE, D. J. (1989). Filtering molecular dynamics trajectories to reveal low-frequency collective motions: phospholipase A2. Journal of Molecular Biology 210, 617-633.
295. SHAM, Y. Y., CHU, Z. T., TAO, H. & WARSHEL, A. (2000). Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Proteins: Structure, Function and Genetics 39, 393-407.
296. SHEA, J.-E. & BROOKS III, C. L. (2001). From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annual Review of Physical Chemistry 52, 499-535.
297. SHEINERMAN, F. B. & BROOKS III, C. L. (1998a). Calculations on folding of segment B1 of streptococcal protein G. Journal of Molecular Biology 278, 439-456.
298. SHEINERMAN, F. B. & BROOKS III, C. L. (1998b). Molecular picture of folding of a small α/β protein. Proceedings of the National Academy of Sciences USA 95, 1562-1567.
299. SHIMADA, J., KANEKO, H., TAKADA, T., KITAMURA, S. & KAJIWARA, K. (2000). Conformation of amylose in aqueous solution: small-angle x-ray scattering measurements and simulations. Journal of Physical Chemistry (B) 104, 2136-2147.
300. SHINODA, W. & MIKAMI, M. (2001). Self-guided molecular dynamics in the isothermal-isobaric ensemble. Chemical Physics Letters 335, 265-272.
301. SHOBANA, S., ROUX, B. & ANDERSEN, O. S. (2000). Free energy simulations: thermodynamics reversibility and variability. Journal of Physical Chemistry (B) 104, 5179-5190.
302. SHROLL, R. M. & SMITH, D. E. (1999). Molecular dynamics simulations in the grand canonical ensemble: formation of a bias potential for umbrella samplng. Journal of Chemical Physics 110, 8295-8302.
303. SIMMERLING, C., MILLER, J. L. & KOLLMAN, P. A. (1998). Combined locally enhanced sampling and particle mesh Ewald as a strategy to locate the experimental structure of a nonhelical nucleic acid. Journal of the American Chemical Society, 120, 7149-7155.
304. SIMONSON, T. (2001). Macromolecular electrostatics: continuum models and their growing pains. Current Opinion in Structural Biology 11, 243-252.
305. - exchange reaction and gas-phase protonation of polyethers. Journal of Computational Chemistry 7, 718-730.
306. SMITH, P. E., BLATT, H. D. & PETTITT, B. M. (1997). On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution. Journal of Physical Chemistry (B) 101, 3886-3890.
307. SMITH, P. E. & PITTITT, B. M. (1995). Efficient Ewald electrostatic calculations for large systems. Computer Physics Communications 91, 339-344.
308. SMITH, P. E. & PITTITT, B. M. (1996). Ewald artifacts in liquid state molecular dynamics simulations. Journal of Chemical Physics 105, 4289-4293.
309. SMITH, P. E. & VAN GUNSTEREN, W. F. (1994). Predictions of free-energy differences from a single simulation of the initial-state. Journal of Chemical Physics 100, 577-585.
310. SMONDYREV, A. M. & BERKOWITZ, M. L. (1999). United atom force field for phospholipid membranes: constant pressure molecular dynamics simulations of dipalmitoylphophatidicholine/water system. Journal of Computational Chemistry 20, 531-545.
311. SOSA, C. P., HEWITT, T., LEE, M. R. & CASE, D. A. (2001). Vectorization of the generalized Born model for molecular dynamics on shared-memory computers. Journal of Molecular Structure: Theochem 549, 193-201.
312. SOUAILLE, M. & ROUX, B. (2001). Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations. Computer Physics Communications 135, 40-57.
313. SPEELMAN, B., BROOKS, B. R. & POST, C. B. (2001). Molecular dynamics simulations of human rhinovirus and an antiviral compound. Biophysical Journal 80, 121-129.
314. SPIESER, S. A. H., VAN KUIK, J. A., KROON-BATENBURG, L. M. J. & KROON, J. (1999). Improved carbohydrate force field for GROMOS: ring and hydroxymethyl group conformational and exo-anomeric effect. Carbohydrate Research 322, 264-273.
315. STEINBACH, P. J. & BROOKS, B. R. (1993). Protein hydration elucidated by molecular dynamics simulation. Proceedings of the National Academy of Sciences USA 90, 9135-9139.
316. STEINBACH, P. J. & BROOKS, B. R. (1994). New spherical-cutoff methods for long-range forces in macromolecular simulation. Journal of Computational Chemistry 15, 667-683.
317. STERN, H. A., KAMINSKI, G. A., BANKS, J. L., ZHOU, R., BERNE, B. J. & FRIESNER, R. A. (1999). Fluctuating charge, polarizable, dipole, and combined models: parameterization from ab initio quantum chemistry. Journal of Physical Chemistry (B) 103, 4730-4737.
318. STOCKER, U. & VAN GUNSTEREN, W. F. (2000). Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMS96 force field against nuclear magnetic resonance data. Proteins: Structure, Function and Genetics 40, 145-153.
319. STOUCH, T. R., WARD, K. B., ALTIERI, A. & HAGLER, A. T. (1991). Simulations of lipid crystals. Characterization of potential energy functions and parameters for lecithin molecules. Journal of Computational Chemistry 12, 1033-1046.
320. STRAATSMA, T. P. & MCCAMMON, J. A. (1992). Computational alchemy. Annual Review of Physical Chemistry 43, 407-435.
321. STRAATSMA, T. P., PHILIPPOPOULOS, M. & MCCAMMON, J. A. (2000). NWChem: exploiting parallelism in molecular simulations. Computer Physics Communications 128, 377-385.
322. STULTZ, C. M. & KARPLUS, M. (1999). MCSS functionality maps for a flexible protein. Proteins: Structure, Function and Genetics 37, 512-529.
323. SUGITA, Y. & OKAMOTO, Y. (1999). Replica-exchange molecular dynamics method for protein folding. Chemical Physics Letters 314, 141-151.
324. TAJKORSHID, E., NOLLERT, P., JENSEN, M. O., MIERKE, L. J. W., O'CONNELL, J., STROUD, R. M. & SCHULTEN, K. (2002). Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296, 525-530.
325. TIELEMAN, D. P. & BERENDSEN, H. J. C. (1996). Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters. Journal of Chemical Physics 105, 4871-4880.
326. TIRADO-RIVES, J. & JORGENSEN, W. L. (1991). Molecular-dynamics simulations of the unfolding of an alpha-helical analog of ribonuclease A S-peptide in water. Biochemistry 30, 3864-3871.
327. TIRADO-RIVES, J. & JORGENSEN, W. L. (1993). Molecular dynamics simulations of the unfolding of apomyoglobin in water. Biochemistry 32, 4175-4184.
328. TIRADO-RIVES, J., OROZCO, M. & JORGENSEN, W. L. (1997). Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry 36, 7313-7329.
329. TIRONI, I. G., SPERB, R., SMITH, P. E. & VAN GUNSTEREN, W. F. (1995). A generalized reaction field method for molecular dynamics simulations. Journal of Chemical Physics 102, 5451-5459.
330. TOBIAS, D. J. (2001). Electrostatic calculations: recent methodological advances and applications to membranes. Current Opinion in Structural Biology 11, 253-261.
331. TOBIAS, D. J., TU, K. C. & KLEIN, M. L. (1997). Atomic-scale molecular dynamcis of lipid membranes. Current Opinion in Colloid Interface Science 2, 15-26.
332. TOUKMAJI, A. Y. & BOARD, J. A. (1996). Ewald summation techniques in perspective: a survey. Computer Physics Communications 95, 73-92.
333. TU, K. C., TOBIAS, D. J. & KLEIN, M. L. (1995). Constant-pressure and temperature molecular-dynamics simulations of crystals of the lecithin fragments - glycerylphosphorylcholine and dilauroylglycerol. Journal of Physical Chemistry 99, 10035-10042.
334. TUCKERMAN, M. E., MARTYNA, G. J. & BERNE, B. J. (1992). Reversible multiple time scale molecular dynamics. Journal of Chemical Physics 97, 1990-2001.
335. TUCKERMAN, M. E. & MARTYNA, G. J. (2000). Understanding modern molecular dynamics: techniques and applications. Journal of Physical Chemistry (B) 104, 159-178. [Additions and corrections (2001), 105, 7598.]
336. TUCKERMAN, M. E., MUNDY, C. J. & MARTYNA, G. J. (1999). On the classical statistical mechanics of non-Hamiltonian systems. Europhysics Letters 45, 149-155.
337. TUCKERMAN, M. E., YARNE, D. A., SAMUELSON, S. O., HUGHES, A. L. & MARTYNA, G. J. (2000). Exploiting multiple levels of parallelism in molecular dynamics based calculations via modern techniques and software paradigms on distributed memory computers. Computer Physics Communications 128, 333-376.
338. VALLEAU, J. P. & COHEN, L. K. (1980). Primitive model electrolytes. I. Grand canonical Monte Carlo computations. Journal of Chemical Physics 72, 5935-5941.
339. VAN DER VAART, A., BURSULAYA, B. D., BROOKS III, C. L. & MERZ JR., K. M. (2000). Are many-body effects important in protein folding? Journal of Physical Chemistry (B) 104, 9554-9563.
340. VAN GUNSTEREN, W. F. & BERENDSEN, H. J. C. (1987). GROningen MOlecular Simulation (GROMOS), library manual. Groningen: Biomos BV.
341. VAN GUNSTEREN, W. F. & BERENDSEN, H. J. C. (1990). Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angewandte Chemie International Edition 29, 992-1023.
342. VAN SCHAIK, R. C., BERENDSEN, H. J. C., TORDA, A. E. & VAN GUNSTEREN, W. F. (1993). A structure refinement method based on molecular dynamics in four spatial dimensions. Journal of Molecular Biology 234, 751-762.
343. VILLÀ, J. & WARSHEL, A. (2001). Energetics and dynamics of enzymatic reactions. Journal of Physical Chemistry (B) 105, 7887-7907.
344. VOROBJEV, Y. N. & HERMANS, J. (1999). A critical analysis of methods of calculation of a potential in simulated polar liquids: strong arguments in favor of 'molecule-based' summation and of vacuum boundary conditions in Ewald summation. Journal of Physical Chemistry (B) 103, 10234-10242.
345. WALL, I. D., LEACH, A. R., SALT, D. W., FORD, M. G. & ESSEX, J. W. (1999). Binding constants of neuraminidase inhibitors: an investigation of the linear interaction energy method. Journal of Medicinal Chemistry 42, 5142-5152.
346. WALSER, R., HÜNENBERGER, P. H. & VAN GUNSTEREN, W. F. (2001). Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal. Proteins: Structure, Function and Genetics 43, 509-519.
347. WANG, J., CIEPLAK, P. & KOLLMAN, P. A. (2000). How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry 21, 1049-1074.
348. WANG, J. & KOLLMAN, P. A. (2001). Automatic parameterization of force field by systematic search and genetic algorithms. Journal of Computational Chemistry 22, 1219-1228.
349. WANG, S. S. & KRUMHANSL, J. A. (1972). Superposition approximation. II. High density fluid argon. Journal of Chemical Physics 56, 4287-4290.
350. WANG, W., DONINI, O., REYES, C. M. & KOLLMAN, P. A. (2001). Biomolecular simulations: recent developments in force field, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annual Review of Biophysical and Biomolecular Structures 30, 211-243.
351. WANG, W., WANG, J. & KOLLMAN, P. A. (1999). What determines the van der Waals coefficient β in the LIE (Linear Interaction Energy) method to estimate binding free energies using molecular dynamics simulations? Proteins: Structure, Function and Genetics 34, 395-402.
352. WARSHEL, A. & LEVITT, M. (1976). Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme. Journal of Molecular Biology 103, 227-249.
353. WEBER, W., HÜNENBERGER, P. H. & McCAMMON, J. A. (2000). Molecular dynamics simulations of a polyalanine octapeptide under Ewald boundary conditions: influence of artificial periodicity on peptide conformation. Journal of Physical Chemistry (B) 104, 3668-3675.
354. WEINER, P. K. & KOLLMAN, P. A. (1981). AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. Journal of Computational Chemistry 2, 287.
355. WEISER, J., SHENKIN, P. S. & STILL, W. C. (1999). Fast, approximate algorithm for detection of solvent-inaccessible atoms. Journal of Computational Chemistry 20, 586-596.
356. WILLIAMS, D. E. (2001). Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals. Journal of Computational Chemistry 22, 1154-1166.
357. WILLIAMS, M. A., THORNTON, J. M. & GOODFELLOW, J. M. (1997). Modelling protein unfolding: hen egg-white lysozyme. Protein Engineering 10, 895-903.
358. WINN, P. J., FERENCZY, G. G. & REYNOLDS, C. A. (1997). Toward improved force fields. 1. Multipole-derived atomic charges. Journal of Physical Chemistry (A) 101, 537-545.
359. WINN, P. J., FERENCZY, G. G. & REYNOLDS, C. A. (1999). Towards improved force field: III. Polarization through modified atomic charges. Journal of Computational Chemistry 20, 704-712.
360. -1 summation. Journal of Chemical Physics 110, 8254-8282.
361. WONG, K.-B., CLARKE, J., BOND, C. J., NEIRA, J. L., FREUND, S. M. V., FERSHT, A. R. & DAGGETT, V. (2000). Towards a complete description of the structural and dynamic properties of the denatured stat of barnase and the role of residual structure in folding. Journal of Molecular Biology 296, 1257-1282.
362. WONG, K.-Y. & PETTITT, B. M. (2000). A new boundary condition for computer simulations of interfacial systems. Chemical Physics Letters 326, 193-198.
363. WOOD, R. H., YEZDIMER, E. M., SAKANE, S., BARRIOCANAL, J. A. & DOREN, D. J. (1999). Free energies of solvation with quantum mechanical interaction energies from classical mechanical simulations. Journal of Chemical Physics 110, 1329-1337.
364. WOODS, R. J. & CHAPPELIE, R. (2000). Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates. Journal of Molecular Structures: Theochem 527, 149-156.
365. WOODS, R. J., DWEK, R. A., EDGE, C. J. & FRASER-RIED, B. (1995). Molecular mechanical and molecular dynamical simulations of glycoproteins and oligosaccharides. 1. GLYCAM-93 parameter development. Journal of Physical Chemistry 99, 3832-3846.
366. WU, X. W. & WANG, S. M. (1998). Self-guided molecular dynamics simulation for efficient conformational search. Journal of Physical Chemistry (B) 102, 7238-7250.
367. YEH, I.-C. & BERKOWITZ, M. L. (1999). Ewald summation for systems with slab geometry. Journal of Chemical Physics 111, 3155-3162.
368. YORK, D. M. & KARPLUS, M. (1999). A smooth solvation potential based on the conductor-like screening model. Journal of Physical Chemistry (A) 103, 11060-11079.
369. YOUNG, M. A., GONFLONI, S., SUPERTI-FURGA, G., ROUX, B. & KURIYAN, J. (2001). Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105, 115-126.
370. ZHANG, L. Y., GALLICCHIO, E., FRIESNER, R. A. & LEVY, R. M. (2001). Solvent models for protein-ligand binding: comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations. Journal of Computational Chemistry 22, 591-607.
371. ZHENG, Y., LEE, T.-S. & YANG, W. (1999). A pseudobond approach to combining quantum mechanical and molecular mechanical methods. Journal of Chemical Physics 110, 46-54.
372. ZHANG, Y., LIU, H. & YANG, W. (2000). Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. Journal of Chemical Physics 112, 3483-3492.
373. ZHOU, J., REICH, S. & BROOKs, B. R. (2000). Elastic molecular dynamics with self-consistent flexible constraints. Journal of Chemical Physics 112, 7919-7929.
374. ZHOU, R., BERNE, B. J. & GERMAIN, R. (2001b). The free energy landscape for β hairpin folding in explicit water. Proceedings of the National Academy of Sciences USA 98, 14931-14936.
375. ZHOU, R., HARDER, E., XU, H. & BERNE, B. J. (2001a). Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems. Journal of Chemical Physics 115, 2348-2358.
376. ZWANZIG, R. W. (1954). High-temperature equation of state by a perturbation method. I. Nonpolar gases. Journal of Chemical Physics 22, 1420-1426.