Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

Computer Physics Communications

Volumn 91, Issue 1-3, 1995, Pages 57-95

  Madura, Jeffry D ^a   Briggs, James M ^b   Wade, Rebecca C ^c   Davis, Malcolm E ^d   Luty, Brock A ^e   Ilin, Andrew ^f   Antosiewicz, Jan ^b   Gilson, Michael K ^g   Bagheri, Babak ^f   Scott, L Ridgway ^f   McCammon, J Andrew ^b  

^a UNIVERSITY OF SOUTH ALABAMA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d BRISTOL MYERS SQUIBB PHARMACEUTICAL RESEARCH INSTITUTE   (United States)

^e ETH ZURICH   (Switzerland)

^f UNIVERSITY OF HOUSTON   (United States)

^g NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Brownian dynamics; Electrostatics; Free energies; Poisson Boltzmann

Indexed keywords

COMPUTER SIMULATION; DIFFUSION; ELECTROSTATICS; FREE ENERGY; MOLECULAR DYNAMICS; MOLECULES; PROTEINS; SUBSTRATES;

BROWNIAN DYNAMICS; POISSON-BOLTZMANN;

COMPUTER SOFTWARE;

EID: 0029633152     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/0010-4655(95)00043-F     Document Type: Article

References (87)

1. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
2. Solving the finite-difference non-linear Poisson-Boltzmann equation
3. A boundary element method for molecular electrostatics with electrolyte effects
4. Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor
5. Incorporating solvent and ion screening into molecular dynamics using the finite-difference Poisson-Boltzmann method
6. The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations
7. Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence
8. Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex.
9. Helix-coil transitions in a simple polypeptide model
10. A Leap-frog Algorithm for Stochastic Dynamics
11. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model
12. Simulation of Bimolecular Reactions
13. The role of mobility in the substrate binding and catalytic machinery of enzymes
14. Solving the finite difference linearized Poisson-Boltzmann equation: A comparison of relaxation and conjugate gradient methods
15. Pfortran
16. Parallel Programming with Guarded Objects
17. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications