Protein molecular dynamics with the generalized Born/ACE solvent model

Proteins: Structure, Function and Genetics

Volumn 45, Issue 2, 2001, Pages 144-158

  Calimet, Nicolas ^a   Schaefer, Michael ^b   Simonson, Thomas ^a,b  

^a INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Computer simulation; Dielectric continuum; Protein structure; Solvation

Indexed keywords

IMMUNOGLOBULIN BINDING FACTOR; PROTEIN G; RAF PROTEIN; RAS PROTEIN; SOLVENT;

AQUEOUS SOLUTION; ARTICLE; CRYSTALLOGRAPHY; DIELECTRIC CONSTANT; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; POLARIZATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIMULATION; SOLVATION; X RAY ANALYSIS;

COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; NERVE TISSUE PROTEINS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-RAF; SOLVENTS;

EID: 0035501755     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.1134     Document Type: Article

References (73)

1. Proteins: A theoretical perspective of dynamics, structure and thermodynamics
2. Implicit solvent models for biomolecular simulations
3. Theoretical methods for the description of the solvent effect in biomolecular systems
4. Macromolecular electrostatics: Continuum models and their growing pains
5. Atomic solvation parameters applied to molecular dynamics of proteins in solution
6. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution
7. Effective energy function for proteins in solution
8. The electrostatic influence of substituents on the dissociation constant of organic acids
9. Electrostatic interactions in macromolecules: Theory and applications
10. Electrostatic contributions to molecular free energies in solution
11. Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann model
12. Accurate calculation of hydration free energies using macroscopic solvent models
13. Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
14. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
15. Microscopic dielectric properties of cytochrome c from molecular dynamics simulations in aqueous solution
16. α's of ionizable residues in proteins: Semi-microscopic and microscopic approaches
17. A Poisson-Boltzmann study of charge insertion in an enzyme active site: The effect of dielectric relaxation
18. Hydrophobic force field as a molecular alternative to surface area models
19. Hydrophobicity at small and large length scales
20. Molecular dynamics simulation with a continuum electrostatic model of the solvent
21. Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model
22. A stochastic dynamics simulation study associated with hydration force and friction memory effect
23. A dielectric continuum molecular dynamics method
24. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
25. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
26. Comparison of generalized Born and Poisson models: Energetics and dynamics of HIV protease
27. Semianalytical treatment of solvation for molecular mechanics and dynamics
28. Generalized Born models of macromolecular solvation effects
29. Continuum electrostatic energies of macromolecules in aqueous solutions
30. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
31. Pairwise descreening of solute charges from a dielectric medium
32. A comprehensive analytical treatment of continuum electrostatics
33. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
34. Generalized Born model based on a surface area formulation
35. Parameterized model for aqueous free energies of solvation using geometry-dependent atomic surface tensions with implicit electrostatics
36. Comparison of a GB solvation model with explicit solvent simulations: Potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane
37. Implicit solvent models: Combining an analytical formulation of continuum electrostatics with simple models of the hydrophobic effect
38. Development of a generalized Born model parameterization for proteins and nucleic acids
39. Solution conformations and thermodynamics of structured peptides: Molecular dynamics simulation with an implicit solvation model
40. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
41. Modification of the generalized Born model suitable for macromolecules
42. Exhaustive docking of molecular fragments with electrostatic solvation
43. Unrestrained simulations of the UUCG tetraloop using an implicit solvation model
44. Molecular dynamics simulations of nucleic acids with a generalized Born model
45. Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models
46. Solution conformations of structured peptides: Continuum electrostatics vs. distance-dependent dielectric functions
47. Effective atom volumes for implicit solvent models: Comparison between Voronoi volumes and minimum fluctuation volumes
48. A molecular dynamics simulation study of segment B1 of protein G
49. Volumen und hydrationswärme der ionen
50. Hydrophobic bonding and accessible surface area in proteins
51. Free energies, enthalpies, and entropies of solution of gaseous nonpolar nonelectrolytes in water and nonaqueous solvents. The hydrophobic effect
52. Charmm: A program for macromolecular energy, minimization, and molecular dynamics calculations
53. Molecular basis for the Born model of solvation
54. Affinities of amino acid side chains for solvent water
55. Solution structures of cyclic and dicyclic analogues of growth hormone releasing factor as determined by two-dimensional NMR and CD spectroscopies and constrained molecular dynamics
56. Polar hydrogen positions in proteins: An empirical energy placement and neutron diffraction comparison
57. Numerical integration of the cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
58. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics program
59. Electrostatics in biomolecular structure and dynamics
60. Calculating electrostatic interactions in bio-molecules: Method and error assessment
61. Environment and exposure to solvent of protein atoms. Lysozyme and insulin
62. Dielectric boundary smoothing in finite-difference solutions of the Poisson equation: An approach to improve accuracy and convergence
63. New spherical-cutoff methods for long-range forces in macromolecular simulation
64. A 500 ps molecular dynamics simulation study of interleukin-1 beta in water: Correlation with nuclear magnetic resonance spectroscopy and crystallography
65. Tanford-Kirkwood electrostatics for protein modeling
66. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
67. Investigation of the backbone dynamics of the IgG-binding domain of streptococcal protein G by heteronuclear two-dimensional 1H-15N nuclear magnetic resonance spectroscopy