Implementation of Accelerated Molecular Dynamics in NAMD.
暂无分享,去创建一个
Klaus Schulten | J Andrew McCammon | Yi Wang | Christopher B Harrison | Christopher B. Harrison | K. Schulten | J. Mccammon | Yi Wang | J. McCammon
[1] Christophe Chipot,et al. Free Energy Calculations , 2008 .
[2] A. Laio,et al. Equilibrium free energies from nonequilibrium metadynamics. , 2006, Physical Review Letters.
[3] M. Gilson,et al. Calculation of protein-ligand binding affinities. , 2007, Annual review of biophysics and biomolecular structure.
[4] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[5] Donald Hamelberg,et al. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study. , 2007, The Journal of chemical physics.
[6] P. Kollman,et al. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .
[7] D. Frenkel. Free-energy calculations , 1991 .
[8] Peter L. Freddolino,et al. Common structural transitions in explicit-solvent simulations of villin headpiece folding. , 2009, Biophysical journal.
[9] A. Voter. Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events , 1997 .
[10] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[11] Donald Hamelberg,et al. A statistical analysis of the precision of reweighting-based simulations. , 2008, The Journal of chemical physics.
[12] Robert V. Swift,et al. Using multistate free energy techniques to improve the efficiency of replica exchange accelerated molecular dynamics , 2009, J. Comput. Chem..
[13] Eric F Darve,et al. Calculating free energies using average force , 2001 .
[14] K. Schulten,et al. Molecular dynamics simulations of membrane channels and transporters. , 2009, Current opinion in structural biology.
[15] Donald Hamelberg,et al. Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis. , 2005, Journal of the American Chemical Society.
[16] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[17] Oliver F. Lange,et al. Flooding in GROMACS: Accelerated barrier crossings in molecular dynamics , 2006, J. Comput. Chem..
[18] A. Voter. A method for accelerating the molecular dynamics simulation of infrequent events , 1997 .
[19] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[20] Grubmüller,et al. Predicting slow structural transitions in macromolecular systems: Conformational flooding. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[21] James Andrew McCammon,et al. Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics , 2009, PLoS Comput. Biol..
[22] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[23] Alexander D. MacKerell,et al. Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..
[24] J. Mongan,et al. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.
[25] G. Bouvignies,et al. Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. , 2007, Journal of the American Chemical Society.
[26] M. Parrinello,et al. Targeting biomolecular flexibility with metadynamics. , 2010, Current opinion in structural biology.
[27] A. Pohorille,et al. Free energy calculations : theory and applications in chemistry and biology , 2007 .
[28] Christophe Chipot,et al. Comprar Free Energy Calculations · Theory and Applications in Chemistry and Biology | Chipot, Christophe | 9783540736172 | Springer , 2007 .
[29] J. Mccammon,et al. Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. , 2007, The Journal of chemical physics.
[30] J. Mccammon,et al. Enhanced Conformational Space Sampling Improves the Prediction of Chemical Shifts in Proteins , 2010, Journal of the American Chemical Society.
[31] J. Mccammon,et al. Toward a Unified Representation of Protein Structural Dynamics in Solution , 2009, Journal of the American Chemical Society.
[32] Donald Hamelberg,et al. Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. , 2005, Journal of the American Chemical Society.
[33] Donald Hamelberg,et al. On the application of accelerated molecular dynamics to liquid water simulations. , 2006, The journal of physical chemistry. B.
[34] César Augusto F. de Oliveira,et al. Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics , 2010, Journal of chemical theory and computation.
[35] J Andrew McCammon,et al. Large conformational changes in proteins: signaling and other functions. , 2010, Current opinion in structural biology.
[36] J. Andrew McCammon,et al. Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations , 2010, Journal of chemical theory and computation.
[37] J. Andrew McCammon,et al. Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration , 2008, Journal of chemical theory and computation.
[38] R Dustin Schaeffer,et al. Combining experiment and simulation in protein folding: closing the gap for small model systems. , 2008, Current opinion in structural biology.
[39] Eric Darve,et al. Adaptive biasing force method for scalar and vector free energy calculations. , 2008, The Journal of chemical physics.
[40] Christophe Chipot,et al. Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. , 2010, Journal of chemical theory and computation.
[41] E. Lindahl,et al. Membrane proteins: molecular dynamics simulations. , 2008, Current opinion in structural biology.