Novel generalized Born methods

The generalized Born (GB) model is a simple continuum dielectric model for the calculation of molecular electrostatic solvation energies. It is a pairwise approximation to the solution of the Poisson equation for continuum electrostatic solvation. Key to the GB method is the calculation of Born radii for every atom in the system. We introduce two new methods for determining Born radii. The first is a two-parameter grid-based method that uses nearly the same molecular volume that is used in conventional Poisson calculations. The second is a five-parameter analytical method that utilizes a molecular volume built from a superposition of atomic functions. The analytical method, distinct from the grid-based algorithm, is amenable to force-based calculations, e.g., energy minimization and molecular dynamics. Unlike other Born radii methods, both algorithms employ a new empirically determined correction term that includes energetic effects beyond the Coulomb field approximation. With this correction term, the gr...

[1]  M. Born.  Volumen und Hydratationswärme der Ionen , 1920 .

[2]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[3]  J. Warwicker,et al.  Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.

[4]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[5]  B. Honig,et al.  Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.

[6]  A. Becke.  A multicenter numerical integration scheme for polyatomic molecules , 1988 .

[7]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[8]  J. Andrew McCammon,et al.  Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation , 1993 .

[9]  Tony You,et al.  An analytical algorithm for the rapid determination of the solvent accessibility of points in a three‐dimensional lattice around a solute molecule , 1995, J. Comput. Chem..

[10]  Gregory D. Hawkins,et al.  Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium , 1996 .

[11]  M. Karplus,et al.  A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .

[12]  Robert G. Parr,et al.  Density Functional Theory of Electronic Structure , 1996 .

[13]  C. Brooks,et al.  A molecular dynamics simulation study of segment B1 of protein G , 1997, Proteins.

[14]  W. C. Still,et al.  The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .

[15]  J. Apostolakis,et al.  Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions , 1997 .

[16]  W. Im,et al.  Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .

[17]  R. Friesner,et al.  Generalized Born Model Based on a Surface Integral Formulation , 1998 .

[18]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[19]  B. Dominy,et al.  Development of a generalized Born model parameterization for proteins and nucleic acids , 1999 .

[20]  D. Case,et al.  Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.

[21]  M. Karplus,et al.  Effective energy functions for protein structure prediction. , 2000, Current opinion in structural biology.

[22]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[23]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution , 2000 .

[24]  R. Lerner,et al.  Blue-fluorescent antibodies. , 2000, Science.

[25]  C. Brooks,et al.  Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase , 2000 .

[26]  J. Andrew Grant,et al.  A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..

[27]  Ray Luo,et al.  Ligand-receptor docking with the Mining Minima optimizer , 2001, J. Comput. Aided Mol. Des..