Second derivatives in generalized Born theory
暂无分享,去创建一个
[1] David J. Wales,et al. Free energy landscapes of model peptides and proteins , 2003 .
[2] P. Kollman,et al. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .
[3] C. Cramer,et al. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.
[4] Tomasz Grycuk,et al. Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation , 2003 .
[5] M. Karplus,et al. Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin. , 1987, Science.
[6] Gregory D. Hawkins,et al. Pairwise solute descreening of solute charges from a dielectric medium , 1995 .
[7] 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 .
[8] D. Truhlar,et al. The incorporation of quantum effects in enzyme kinetics modeling. , 2002, Accounts of chemical research.
[9] P. Jørgensen,et al. Walking on potential energy surfaces , 1983 .
[10] D. Case,et al. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. , 2003, Journal of molecular biology.
[11] Nathan A. Baker,et al. Poisson-Boltzmann Methods for Biomolecular Electrostatics , 2004, Numerical Computer Methods, Part D.
[12] D. Dunlap,et al. Positively charged surfaces increase the flexibility of DNA. , 2005, Biophysical journal.
[13] István Kolossváry,et al. Low‐mode conformational search elucidated: Application to C39H80 and flexible docking of 9‐deazaguanine inhibitors into PNP , 1999 .
[14] Charles L. Brooks,et al. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures , 2004, J. Comput. Chem..
[15] R Diamond,et al. On the use of normal modes in thermal parameter refinement: theory and application to the bovine pancreatic trypsin inhibitor. , 1990, Acta crystallographica. Section A, Foundations of crystallography.
[16] D. Case,et al. Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.
[17] F. A. Neugebauer,et al. Electrochemical oxidation and structural changes of 5,6-dihydrobenzo[c]cinnolines , 1996 .
[18] A Kitao,et al. Energy landscape of a native protein: Jumping‐among‐minima model , 1998, Proteins.
[19] David J Wales,et al. Archetypal energy landscapes: dynamical diagnosis. , 2005, The Journal of chemical physics.
[20] D. Case,et al. Modification of the Generalized Born Model Suitable for Macromolecules , 2000 .
[21] W. Miller,et al. ON FINDING TRANSITION STATES , 1981 .
[22] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[23] D. Case,et al. Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model , 2000 .
[24] Ron Elber,et al. Reaction path study of helix formation in tetrapeptides: Effect of side chains , 1991 .
[25] N. Go,et al. Investigating protein dynamics in collective coordinate space. , 1999, Current opinion in structural biology.
[26] David A. Case,et al. Vectorization of the generalized Born model for molecular dynamics on shared-memory computers , 2001 .
[27] Thomas Simonson,et al. Electrostatics and dynamics of proteins , 2003 .
[28] A. Mattevi,et al. Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase. , 2000, Structure.
[29] G. S. Manning. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides , 1978, Quarterly Reviews of Biophysics.
[30] I. Schlichting,et al. Crystal structure of cytochrome P‐450cam complexed with the (1S)‐camphor enantiomer , 1997, FEBS letters.
[31] K. Struhl,et al. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α Helices: Crystal structure of the protein-DNA complex , 1992, Cell.
[32] P. Beroza,et al. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects , 1999 .
[33] M. Karplus,et al. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics , 1997 .
[34] J. Ramstein,et al. Energetic coupling between DNA bending and base pair opening. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[35] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[36] Atsushi Matsumoto,et al. Dynamic properties of double-stranded DNA by normal mode analysis , 1999 .
[37] P. S. Kim,et al. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. , 1991, Science.
[38] M. J. Bennett,et al. Steroid recognition and regulation of hormone action: crystal structure of testosterone and NADP+ bound to 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase. , 1997, Structure.
[39] A. Bondi. van der Waals Volumes and Radii , 1964 .
[40] B. Masters,et al. Three-dimensional structure of NADPH-cytochrome P450 reductase: prototype for FMN- and FAD-containing enzymes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[41] Ronald M. Levy,et al. AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling , 2004, J. Comput. Chem..
[42] D. Beveridge,et al. A MODIFICATION OF THE GENERALIZED BORN THEORY FOR IMPROVED ESTIMATES OF SOLVATION ENERGIES AND PK SHIFTS , 1998 .
[43] D. Case. Normal mode analysis of protein dynamics , 1994 .
[44] Peter Scheffel,et al. Incorporating variable dielectric environments into the generalized Born model. , 2005, The Journal of chemical physics.
[45] Michael Feig,et al. Implicit solvation based on generalized Born theory in different dielectric environments. , 2004, The Journal of chemical physics.
[46] Case,et al. Collective NMR relaxation model applied to protein dynamics. , 1994, Physical review letters.
[47] Holger Gohlke,et al. Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf , 2004, J. Comput. Chem..
[48] D. Case,et al. Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.
[49] David A. Case,et al. Effective Born radii in the generalized Born approximation: The importance of being perfect , 2002, J. Comput. Chem..
[50] P. Kollman,et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.
[51] M. Schaefer,et al. A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. , 1990, Journal of molecular biology.