Current status of the AMOEBA polarizable force field

Journal of Physical Chemistry B

Volumn 114, Issue 8, 2010, Pages 2549-2564

  Ponder, Jay W ^a   Wu, Chuanjie ^a   Ren, Pengyu ^b   Pande, Vijay S ^c   Chodera, John D ^c   Schnieders, Michael J ^c   Haque, Imran ^c   Mobley, David L ^d   Lambrecht, Daniel S ^e   Distasio Jr , Robert A ^e   Head Gordon, Martin ^e   Clark, Gary N I ^f   Johnson, Margaret E ^f   Head Gordon, Teresa ^f  

^a WASHINGTON UNIVERSITY   (United States)

^b The University of Texas at Austin   (United States)

^c Stanford University   (United States)

^d UNIVERSITY OF NEW ORLEANS   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f University of California at Berkeley   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ELECTRONIC STRUCTURE; ISOMERS; MOLECULES; PROTOZOA; SULFUR COMPOUNDS;

AROMATIC INTERACTIONS; CONFORMATIONAL ENERGIES; DYNAMICAL PROPERTIES; ELECTRONIC STRUCTURE CALCULATIONS; MOLECULAR FORCE FIELD; POLARIZABLE FORCE FIELD; SOLVATION FREE ENERGIES; THEORETICAL MODELING;

X RAY CRYSTALLOGRAPHY;

EID: 77749298172     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp910674d     Document Type: Article

References (104)

1. Ponder, J. W.; Case, D. A. Force fields for protein simulations. Protein Simul. 2003, 66, 27+.
2. MacKerell, A. D. J. Empirical Force Fields for Biological Macromolecules: Overview and Issues. J. Comput. Chem. 2004, 25, 1584-1604.
3. a) Halgren, T. A.; Damm, W. Polarizable Force Fields. Curr. Opin. Struct. Biol. 2001, 11, 236-242.
4. b) Rick, S. W.; Stuart, S. J. Potentials and Algorithms for Incorporating Polarizability in Computer Simulations. Rev. Comput. Chem. 2002, 18, 89-146.
5. c) Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A.; Cao, Y. X.; Murphy, R. B.; Zhou, R.; Halgren, T. A. Development of a polarizable force field for Proteins via ab initio quantum chemistry: first generation model and gas phase tests. J. Cormput. Chem. 2002, 23, 1515-1531.
6. d) Kaminski, G. A.; Stern, H. A.; Berne, B. J.; Friesner, R. A. Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry. J. Phys. Chem. A 2004, 108 (4), 621-627.
7. e) Patel, S.; Brooks, C. L., 3rd. CHARMM. fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations, J. Comput. Chem. 2004, 25 (1), 1-15.
8. f) Patel, S.; Mackerell, A. D., Jr.; Brooks, C. L., III CHARMM. fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comput. Chem. 2004, 25 (12), 1504-1514.
9. g) Harder, E.; Kim, B. C.; Friesner, R. A.; Berne, B. J. Efficient simulation method for polarizable protein force fields: application to the simulation of BPTI in liquid. J. Chem. Theory Comput. 2005, 1, 169-180.
10. h) Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; Mackerell, A. D., Jr. A polarizable model of water for molecular dynamics simulations of biomolecules. Chem. Phys. Lett. 2006, 418, 245-249. (Pubitemid 43063383)
11. i) Wang, Z. X.; Zhang, W.; Wu, C.; Lei, H.; Cieplak, P.; Duan, Y. Strike a balance: optimization, of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J. Comput. Chem. 2006, 27 (6), 781-790.
12. j) Cieplak, P.; Dupradeau, F.-Y.; Duan, Y.; Wang, J. Polarization Effects in. Molecular Mechanical Force Fields. J. Phys.: Condens. Matter 2009, 21, 333102.
13. Ponder, J. W. TINKER: Software Tools for Molecular Design, 5.0; Washington University School of Medicine: Saint Louis, MO, 2009.
14. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber BioMolecular Simulation Programs. J. Comput. Chem. 2005, 26, 1668-1688.
15. Brooks, B. R.; Brooks, C. L., 3rd; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M..; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 2009, 30 (10), 1545-1614.
16. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. j. Chem. Theory Comput. 2008, 4, 435-447.
17. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26 (16), 1781-1802.
18. a) Corongiu, G. Molecular Dynamics Simulation for Liquid Water Using a Polarizable and Flexible Potential. Int. J. Quantum Chem. 1992, 42, 1209-1235.
19. b) Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum, mechanical calculations. J. Comput. Chem. 2003, 24 (16), 1999-2012.
20. c) Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006, 65 (3), 712-725. (Pubitemid 44583220)
21. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; JosephMcCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom, empirical potential for molecular modeling and dynamics studies of proteins. J. Phvs. Chem. B 1998, 102 (18), 3586-3616. (Pubitemid 128576688)
22. a) van Gunsteren, W. F.; Daura, X.; Mark, A. E. GROMOS Force Field. Encyclopedia of Computational Chemistry 1998, 2, 1211-1216.
23. b) Oostenbrink, C.; Villa, A.; Mark, A. E.; van Gunsteren, W. F. A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25 (13), 1656-1676.
24. a) Jorgensen, W. L.; Tirado-Rives, J. The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657-1666.
25. b) Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. Development and testing of the OPLS allatom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118 (45), 11225-11236.
26. c) Kaminski, G.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison, with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105, 6474-6487.
27. a) Ren, P. Y.; Ponder, J. W. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 2002, 23 (16), 1497-1506.
28. b) Ren, P. Y.; Ponder, J. W. Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B 2003, 107 (24), 5933-5947.
29. c) Grossfield, A.; Ren, P. Y.; Ponder, J. W. Ion solvation thermodynamics from simulation with, a polarizable force field. J. Am. Chem. Soc. 2003, 125 (50), 15671-15682.
30. d) Ren, P. Y.; Ponder, J. W. Temperature and pressure dependence of the AMOEBA water model, J. Phys. Chem. B 2004, 108 (35), 13427-13437.
31. e) Ren, P.; Wu, C.; Ponder, J. W. Polarizable atomic multipole-based intermolecular potentials for organic molecules. J. Chem. Theory Comput. 2010, submitted.
32. Gresh, N.; Cisneros, G. A.; Darden, T. A.; Piquemal, J.-P. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J. Chem. Theory Comput. 2007, 3, 1960-1986.
33. Astrand, P.-O.; Linse, P.; Karlstrom, G. Molecular dynamics study of water adopting a potential function with explicit atomic dipole moments and anisotropic polarizabilities. Chem. Phys. 1995, 191, 195-202.
34. Swart, M.; van Duijnen, P. T. DRF90: A Polarizable Force Field. Mol. Simul. 2006, 32, 471-484.
35. a) Thole, B. T. Molecular Polarizabilities Calculated with a Modified Dipole Interaction. Chem. Phys. 1981, 59, 341-350.
36. b) van Duijnen, P. T.; Swart, M. Molecular and Atomic Polarizabilities: Thole's Model Revisited, J. Phys. Chem. A 1998, 102 (14), 2399-2407.
37. Allinger, N. L.; Yuh, Y. H.; Lii, J. H. Molecular Mechanics. The MM3 Force-Field for Hydrocarbons 0.1. J. Am. Chem. Soc. 1989, 111 (23), 8551-8566.
38. Wilson, E. B.; Decius, J. C.; Cross, P. C. Molecular Vibrations; McGraw-Hill: New York, 1955.
39. Bell, R. P. Bond Torsion in the Vibrations of the Benzene Molecule. Trarns. Faraday Soc. 1945, 41, 293b-295.
40. Mannfors, B.; Sundius, T.; Palmo, K.; Pietila, L. O.; Krimm, S. Spectroscopically determined force fields for macromolecules. Part 3. Alkene chains, J. Mol. Struct. 2000, 522, 49-75. (Pubitemid 30237678)
41. vdW Parameters, J. Am. Chem. Soc. 1992, 114, 7827-7843.
42. Stewart, R. F.; Davidson, E. R.; Simpson, W. T. Coherent X-Ray Scattering of the Hydrogen Atom in the Hydrogen Molecule. J. Chem. Phys. 1965, 42 (9), 3175-3187.
43. Coppens, P.; Guru Row, T. N.; Leung, P.; Stevens, E. D.; Becker, P. J.; Yang, Y. W. Net Atomic Charges and Molecular Dipole Moments from Spherical-Atom X-Ray Refinements, and the Relation between Atomic Charge and Shape. Acta Crystallogr. 1979, A35 (1), 63-72.
44. a) Dykstra, C. E. Efficient Calculation of Electrically Based Intermolecular Potentials of Weakly Bonded Clusters. J. Comput. Chem. 1988, 9, 476-487.
45. b) Applequist, J. Traceless Cartesian Tensor Forms for Spherical Harmonic-Functions - New Theorems and Applications to Electrostatics of Dielectric Media, J. Phys. A: Math. Gen. 1989, 22 (20), 4303-4330.
46. a) Stone, A. J. Distributed Multipole Analysis, or How to Describe a Molecular Charge Distribution. Chem. Phys. Lett. 1981, 83 (2), 233239.
47. b) Stone, A. J. Distributed Multipole Analysis: Stability for Large Basis Sets. J. Chem. Theory Comput. 2005, 1, 1128-1132.
48. Kong, Y. Multipole Electrostatic Methods for Protein Modeling with Reaction Field Treatment. Ph.D. thesis, Washington University Medical School, St. Louis, MO, 1997.
49. Stone, A. J. The Theory of Intermolecular Forces; Oxford University Press: Oxford, U.K., 1996.
50. Burnham, C. J.; Li, J. C.; Xantheas, S. S.; Leslie, M. The Parametrization of a Thole-type All-Atom. Polarizable Water Model from First Principles and Its Application to the Study of Water Clusters (n=221) and the Phonon Spectrum of Ice Ih. J. Chem. Phys. 1999, 110 (9), 4566-4581. (Pubitemid 129615508)
51. Morita, A. Water polarizability in condensed phase: Ab initio evaluation by cluster approach. J. Comput. Chem. 2002, 23 (15), 14661471. (Pubitemid 35359089)
52. Morita, A.; Kato, S. An ab initio analysis of medium, perturbation on molecular polarizabilities. J. Chem. Phys. 1999, 110 (24), 11987-11998.
53. Gubskaya, A. V.; Kusalik, P. G. The multipole polarizabilities and hyperpolarizabilities of the water molecule in liquid state: an ab initio study. Mol. Phys. 2001, 99 (13), 1107-1120.
54. a) Gubskaya, A. V.; Kusalik, P. G. The total molecular dipole moment for liquid water, J. Chem. Phys. 2002, 117 (11), 5290-5302.
55. b) Silvestrelli, P. L.; Parrinello, M. Water Molecule Dipole in the Gas and in the Liquid Phase. Phys. Rev. Lett. 1999, 82 (16), 3308-3311. (Pubitemid 129689259)
56. Head-Gordon, M.; Artacho, E. Chemistry on the Computer. Phys. Today 2008, 61, 58-63.
57. Helgaker, T.; Klopper, W.; Tew, D. P. Quantitative Quantum Chemistry. Mol. Phys. 2008, 106, 2107-2143.
58. Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields, J. Am. Chem. Soc. 1997, 119 (25), 5908-5920.
59. a) DiStasio, R. A.; Jung, Y.; Head-Gordon, M. A Resolution-OfThe-Identity Implementation of the Local Triatomics-In-Molecules Model for Second-Order Møller-Plesset Perturbation Theory with Application to Alanine Tetrapeptide Conformational Energies. J. Chem. Theory Comput. 2005, 1, 862-876.
60. b) DiStasio, R. A., Jr.; Steele, R. P.; Rhee, Y. M.; Shao, Y.; Head-Gordon, M. An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Moller-Plesset perturbation theory: application to alanine tetrapeptide conformational analysis. J. Comput. Chem. 2007, 28 (5), 839-856. (Pubitemid 46491693)
61. Chai, J.-D.; Head-Gordon, M. Systematic optimization of longrange corrected hybrid density functionals. J. Chem. Phys. 2008, 128, 084106. (Pubitemid 351328681)
62. Chai, J.-D.; Head-Gordon, M. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys. Chem. Chem. Phys. 2008, 10, 6615-6620.
63. Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins. J. Chem. Phys. 2003, 119, 5740-5761.
64. a) Bennett, C. H. Efficient Estimation of Free Energy Differences from Monte Carlo Data, J. Comput. Phys. 1976, 22, 245-268.
65. b) Jiao, D.; King, C.; Grossfield, A.; Darden, T. A.; Ren, P. Y. Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J. Phys. Chem. B 2006, 110 (37), 18553-18559.
66. c) Shirts, M. R.; Bair, E.; Hooker, G.; Pande, V. S. Equilibrium free energies from nonequilibrium measurements using maximum likelihood methods. Phys. Rev. Lett. 2003, 91 (14), 140601-140604.
67. a) Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group contribution to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution. J. Solution Chem. 1981, 10, 563-595.
68. b) Wolfenden, R.; Liang, Y.-L.; Matthews, M.; Williams, R. Cooperativity and anticooperativity in solvation by water: imidazoles, quinones, nitrophenols, nitrophenolate, and nitrothiophenolate ions. J. Am. Chem. Soc. 1987, 109 (2), 463-466.
69. c) Wolfenden, R. Interaction of the peptide bond with solvent water: A vapor phase analysis. Biochemistry 1978, 17, 201-204. (Pubitemid 8257970)
70. d) Abraham, M. H.; Whiting, G. S. Thermodynamics of solute transfer from water to hexadecane. J. Chem. Soc. Perkin Trans 1990, 2, 291-300.
71. Nicholls, A.; Mobley, D. L.; Guthrie, J. P.; Chodera, J. D.; Bayly, C. I.; Cooper, M. D.; Pande, V. S. Predicting small-molecule solvation free energies: An informal blind test for computational chemistry. J. Med. Chem. 2008, 51 (4), 769-779.
72. Mobley, D. L.; Dumont, E.; Chodera, J. D.; Dill, K. A. Comparison of charge models for fixed-charge forcefields: small molecule hydration, free energies in explicit solvent. J. Phys. Chem. B 2007, 111, 2242-2254.
73. Shirts, M. R.; Mobley, D. L.; Chodera, J. D.; Pande, V. S. Accurate and efficient corrections for missing dispersion interactions in Molecular Simulations, J. Phys. Chem. B 2007, 111, 13052-13063.
74. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular-Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81, 3684-3690.
75. Minh, D. D. L.; Chodera, J. D. Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. J. Chem. Phys. 2009, 131, 134110.
76. Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group Contributions to the Thermodynamic Properties of Non-Ionic Organic Solutes in Dilute Aqueous Solution. J. Solution Chem. 1981, 10, 563-595.
77. a) Johnson, M. E.; Malardier-Jugroot, C.; Murarka, R. K.; HeadGordon, T. Hydration water dynamics near biological interfaces. J. Phys. Chem. B 2009, 113, 4082-4092.
78. b) Johnson, M. E.; Malardier-Jugroot, C.; Head-Gordon, T. Effects of co-solvents on peptide hydration water structure and dynamics. Phys. Chem. Chem. Phys. 2010, 12 (2), 393-405.
79. c) Malardier-Jugroot, C.; Bowron, D. T.; Soper, A. K.; Johnson, M. E.; Head-Gordon, T. Structure and dynamics of aqueous peptide solutions in the presence of co-solvents. Phys. Chem. Chem. Phys. 2010, 12 (2), 382392.
80. d) Malardier-Jugroot, C.; Head-Gordon, T. Separable cooperative and localized translations motions of water confined by a chemically heterogeneous environment. Phys. Chem. Chem. Phys. 2007, 9 (16), 1962-1971.
81. e) Malardier-Jugroot, C.; Johnson, M. E.; Murarka, R. K.; Head-Gordon, T. Aqueous peptides as experimental models for hydration water dynamics near protein surfaces. Phys. Chem. Chem. Phys. 2008, 10 (32), 4903-4908.
82. Horn, H. W.; Swope, W. C.; Pitera, J. W.; Madura, J. D.; Dick, T. J.; Hura, G. L.; Head-Gordon, T. Development of an improved four-site water model for bio-molecular simulations: TIP4P-Ew. J. Chem. Phys. 2004, 120 (20), 9665-9678.
83. a) Marcus, Y. Effect of ions on the structure of water: Structure making and breaking. Chem. Rev. 2009, 109, 1346-1370.
84. b) Auton, M.; Bolen, D. W.; Rösgen, J. Structural thermodynamics of protein preferential solvation: osmolyte solvation of Proteins, aminoacids and peptides. Proteins 2008, 73 (4), 802-813.
85. Timasheff, S. N. The Control of Protein Stability and Association by Weak-Interactions with Water - How Do Solvents Affect These Processes. Annu. Rev. Biophys. Biomol. Struct. 1993, 22, 67-97. (Pubitemid 23180317)
86. (a) Jiao, D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Calculation of protein-ligand binding free energy by using a polarizable potential. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6290-6295. (Pubitemid 351758339)
87. b) Jiao, D.; Zhang, J.; Duke, R. E.; Li, G.; Schnieders, M. J.; Ren, P. Trypsin-Ligand Binding Free Energies from Explicit and Implicit Solvent Simulations with Polarizable Potential, J. Comput. Chem. 2009, 30, 1701-1711.
88. c) Shi, Y.; Jiao, D.; Schnieders, M. J.; Ren, P. Trypsin-Ligand Binding Free Energy Calculation with AMOEBA. IEEE Engineering in Medicine and Biology Society 2009, EMBC proceedings, 2328-2331.
89. Katz, B. A.; Finer-Moore, J.; Mortezaei, R.; Rich, D. H.; Stroud, R. M. Episelection - Novel K-I-Similar-to Nanomolar Inhibitors of Serine Proteases Selected by Binding or Chemistry on an Enzyme Surface. Biochemistry 1995, 34, 8264-8280.
90. a) Boresch, S.; Karplus, M. Absolute binding free energies: A quantitative approach for their calculation. J. Phys. Chem. B 2003, 107, 9535-9551.
91. b) Hamelberg, D.; McCammon, J. A. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method. J. Am. Chem. Soc. 2004, 126, 7683-7689.
92. (a) Katz, B. A.; Elroda, K.; Luonga, C.; Ricea, M. J.; Mackmana, R. L.; Sprengelera, P. A.; Spencera, J.; Hatayea, J.; Janea, J.; Linka, J.; Litvaka, J.; Raia, R.; Ricea, K.; Siderisa, S.; Vernera, E.; Young, W. A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J. Mol. Biol. 2001, 307, 1451-1486. (Pubitemid 33027652)
93. b) Schwarzl, S. M.; Tschopp, T. B.; Smith, J. C.; Fischer, S. Can the calculation, of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J. Comput. Chem. 2002, 23, 1143-1149. (Pubitemid 34854445)
94. Brunger, A. T. Version 1.2 of the Crystallography and NMR system. Nat. Protoc. 2007, 2, 2728.
95. Adams, P. D.; Grosse-Kunstleve, R. W.; Hung, L. W.; Loerger, T. R.; McCoy, A. J.; Moriarty, N. W.; Read, R. J.; Sacchettini, J. C.; Sauter, N. K.; Terwilliger, T. C. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr., Sect. D 2002, 58, 1948.
96. a) Sagui, C.; Pedersen, L. G.; Darden, T. A. Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations, J. Chem. Phys. 2004, 120, 73.
97. b) Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method, J. Chem. Phys. 1995, 103, 8577.
98. c) Darden, T.; York, D.; Pedersen, L. Particle mesh ewald: An n log(n) method for ewald sums. J. Chem. Phys. 1993, 98, 10089.
99. Schnieders, M. J.; Fenn, T. D.; Pande, V. S.; Brunger, A. T. Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallogr., Sect. D 2009, 65, 952.
100. Fenn, T. D.; Schnieders, M. J.; Brunger, A. T.; Pande, V. S. J. Mol. Biol., submitted for publication, 2009.
101. Larson, S. M.; Snow, C.; Pande, V. S. Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology; Horizon Press: New York, 2003.
102. Tishchenko, O.; Higashi, M.; Albu, T. V.; Corchado, J. C.; Kim, Y.; Vill, J.; Xing, J.; Lin, H.; Truhlar, D. G. MC-Tinker; University of Minnesota: Minneapolis, MN, 2009.
103. Gordon; M. S. Schmidt, M. W. Advances in electronic structure theory: GAMESS a decade later; Elsevier: Amsterdam, The Netherlands, 2005.
104. Friedrichs, M.; Eastman, P.; Vaidyanathan, V.; Houston, M.; LeGrand, S.; Beberg, A.; Ensign, D.; Bruns, C.; Pande, V. S. Accelerating Molecular Dynamic Simulation on Graphics Processing Units, J. Comput. Chem. 2009, 30, 864-872.