The Multiscale Coarse- Graining Method: A Systematic Approach to Coarse-Graining

[1]  Gregory A Voth,et al.  Multiscale coarse-graining of monosaccharides. , 2007, The journal of physical chemistry. B.

[2]  Gregory A Voth,et al.  Coarse-grained peptide modeling using a systematic multiscale approach. , 2007, Biophysical journal.

[3]  Gregory A Voth,et al.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory. , 2007, The journal of physical chemistry. B.

[4]  Gregory A Voth,et al.  Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.

[5]  Gregory A Voth,et al.  Are many-body electronic polarization effects important in liquid water? , 2007, The Journal of chemical physics.

[6]  Gregory A Voth,et al.  Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. , 2007, The Journal of chemical physics.

[7]  Jhih-Wei Chu,et al.  Emerging methods for multiscale simulation of biomolecular systems , 2007 .

[8]  Gregory A. Voth,et al.  Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations , 2006, Proceedings of the National Academy of Sciences.

[9]  Qiang Shi,et al.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. , 2006, The journal of physical chemistry. B.

[10]  Ralf Langen,et al.  Mechanism of endophilin N‐BAR domain‐mediated membrane curvature , 2006, The EMBO journal.

[11]  Soichi Takeda,et al.  Endophilin BAR domain drives membrane curvature by two newly identified structure‐based mechanisms , 2006, The EMBO journal.

[12]  Gregory A Voth,et al.  Multiscale coarse-graining of ionic liquids. , 2006, The journal of physical chemistry. B.

[13]  Gregory A. Voth,et al.  The multiscale challenge for biomolecular systems: coarse-grained modeling , 2006 .

[14]  Peter L. Freddolino,et al.  Molecular dynamics simulations of the complete satellite tobacco mosaic virus. , 2006, Structure.

[15]  Gregory A Voth,et al.  Computer simulation of proton solvation and transport in aqueous and biomolecular systems. , 2006, Accounts of chemical research.

[16]  Sharon Hammes-Schiffer,et al.  Hydrogen tunneling and protein motion in enzyme reactions , 2006, Accounts of chemical research.

[17]  Akihiro Kusumi,et al.  Toward understanding the dynamics of membrane-raft-based molecular interactions. , 2005, Biochimica et biophysica acta.

[18]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[19]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[20]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[21]  S. Joseph,et al.  Simulating movement of tRNA into the ribosome during decoding. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  I. Bahar,et al.  Coarse-grained normal mode analysis in structural biology. , 2005, Current opinion in structural biology.

[23]  Gregory A Voth,et al.  Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation. , 2005, The journal of physical chemistry. B.

[24]  G. Voth,et al.  Unique spatial heterogeneity in ionic liquids. , 2005, Journal of the American Chemical Society.

[25]  Valentina Tozzini,et al.  Coarse-grained models for proteins. , 2005, Current opinion in structural biology.

[26]  Gregory A Voth,et al.  A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.

[27]  Eric Jakobsson,et al.  Simulation of the early stages of nano-domain formation in mixed bilayers of sphingomyelin, cholesterol, and dioleylphosphatidylcholine. , 2004, Biophysical journal.

[28]  Gregory A Voth,et al.  Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. , 2004, The Journal of chemical physics.

[29]  D Thirumalai,et al.  Continuous anisotropic representation of coarse-grained potentials for proteins by spherical harmonics synthesis. , 2004, Journal of molecular graphics & modelling.

[30]  Willy Wriggers,et al.  Spanning the length scales of biomolecular simulation. , 2004, Structure.

[31]  A. Mark,et al.  Coarse grained model for semiquantitative lipid simulations , 2004 .

[32]  Grace Brannigan,et al.  Solvent-free simulations of fluid membrane bilayers. , 2004, The Journal of chemical physics.

[33]  J. Frank,et al.  Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[34]  S Gnanakaran,et al.  Peptide folding simulations. , 2003, Current opinion in structural biology.

[35]  Florence Tama,et al.  Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. , 2003, Journal of molecular biology.

[36]  V. Pande,et al.  Absolute comparison of simulated and experimental protein-folding dynamics , 2002, Nature.

[37]  J. Berg,et al.  Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.

[38]  Arieh Warshel,et al.  Molecular dynamics simulations of biological reactions. , 2002, Accounts of chemical research.

[39]  J Mervis NSF Launches TeraGrid for Academic Research , 2001, Science.

[40]  A. Liwo,et al.  Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field , 2001 .

[41]  X. Daura,et al.  The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State. , 2001, Angewandte Chemie.

[42]  Kai Simons,et al.  Lipid rafts and signal transduction , 2000, Nature Reviews Molecular Cell Biology.

[43]  E. Lindahl,et al.  Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. , 2000, Biophysical journal.

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

[45]  P. B. Warren,et al.  DISSIPATIVE PARTICLE DYNAMICS : BRIDGING THE GAP BETWEEN ATOMISTIC AND MESOSCOPIC SIMULATION , 1997 .

[46]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[47]  W Smith,et al.  DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. , 1996, Journal of molecular graphics.

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

[49]  M. Levitt A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[50]  M. Levitt,et al.  Computer simulation of protein folding , 1975, Nature.

[51]  Frank L. H. Brown,et al.  Implicit solvent simulation models for biomembranes , 2005, European Biophysics Journal.

[52]  Klaus Schulten,et al.  Multiscale Method for Simulating Protein-DNA Complexes , 2004, Multiscale Model. Simul..

[53]  Daniel A. Reed,et al.  Grids, the TeraGrid, and Beyond , 2003, Computer.

[54]  Bernard R Brooks,et al.  A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy. , 2003, Journal of structural biology.