Multiscale modeling of biomolecular systems: in serial and in parallel.
暂无分享,去创建一个
Gregory A Voth | Gary S Ayton | Will G Noid | G. Voth | W. Noid | G. Ayton
[1] 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.
[2] Cecilia Clementi,et al. Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go? , 2004, Journal of molecular biology.
[3] Jianpeng Ma,et al. Refinement of F-actin model against fiber diffraction data by long-range normal modes. , 2004, Biophysical journal.
[4] J. Straub,et al. Coarse-Grained Model of Coil-to-Helix Kinetics Demonstrates the Importance of Multiple Nucleation Sites in Helix Folding. , 2006, Journal of chemical theory and computation.
[5] John E Straub,et al. Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials. , 2005, The Journal of chemical physics.
[6] Cezary Czaplewski,et al. Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. , 2006, Journal of chemical theory and computation.
[7] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[8] E. Shakhnovich,et al. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[9] Taner Z Sen,et al. The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. , 2006, Journal of chemical theory and computation.
[10] Marilisa Neri,et al. Coarse-grained model of proteins incorporating atomistic detail of the active site. , 2005, Physical review letters.
[11] Kurt Kremer,et al. Tunable generic model for fluid bilayer membranes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.
[12] Gregory A Voth,et al. Coarse-grained peptide modeling using a systematic multiscale approach. , 2007, Biophysical journal.
[13] Jianpeng Ma,et al. Substructure synthesis method for simulating large molecular complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[14] Gregory A Voth,et al. Modeling real dynamics in the coarse-grained representation of condensed phase systems. , 2006, The Journal of chemical physics.
[15] David Swigon,et al. Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[16] Edward Lyman,et al. Resolution Exchange Simulation with Incremental Coarsening. , 2006, Journal of chemical theory and computation.
[17] Gregory A Voth,et al. A second generation mesoscopic lipid bilayer model: connections to field-theory descriptions of membranes and nonlocal hydrodynamics. , 2006, The Journal of chemical physics.
[18] Feng Ding,et al. Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. , 2005, Journal of molecular biology.
[19] Alexander P. Lyubartsev,et al. Effective potentials for ion-DNA interactions , 1999 .
[20] Eugene I. Shakhnovich,et al. A structure-based method for derivation of all-atom potentials for protein folding , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[21] Gregory A Voth,et al. Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes. , 2007, The Journal of chemical physics.
[22] Siewert J Marrink,et al. The mechanism of vesicle fusion as revealed by molecular dynamics simulations. , 2003, Journal of the American Chemical Society.
[23] R Lavery,et al. From atomic to mesoscopic descriptions of the internal dynamics of DNA. , 1999, Biophysical journal.
[24] Daniel M. Zuckerman,et al. Simulation of an Ensemble of Conformational Transitions in a United-Residue Model of Calmodulin , 2004 .
[25] Wilma K Olson,et al. Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 1. Comparison of Computed Motions with the Predicted Behavior of an Ideal Elastic Rod. , 2005, Journal of chemical theory and computation.
[26] Robert L Jernigan,et al. Comparison of tRNA motions in the free and ribosomal bound structures. , 2005, Biophysical journal.
[27] 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 .
[28] I. Bahar,et al. Gaussian Dynamics of Folded Proteins , 1997 .
[29] Valentina Tozzini,et al. Coarse-grained models for proteins. , 2005, Current opinion in structural biology.
[30] N. Go,et al. Respective roles of short- and long-range interactions in protein folding. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[31] Stephen C Harvey,et al. Packaging double‐helical DNA into viral capsids , 2004, Biopolymers.
[32] Sergei Izvekov,et al. Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers. , 2006, Journal of chemical theory and computation.
[33] Klaus Schulten,et al. Multiscale Method for Simulating Protein-DNA Complexes , 2004, Multiscale Model. Simul..
[34] Gregory A Voth,et al. A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.
[35] S. Feller,et al. Molecular dynamics simulations of lipid bilayers , 2000 .
[36] Jianpeng Ma,et al. A New Method for Coarse-Grained Elastic Normal-Mode Analysis. , 2006, Journal of chemical theory and computation.
[37] M. Stevens,et al. Coarse-grained simulations of lipid bilayers. , 2004, The Journal of chemical physics.
[38] Edward Lyman,et al. Resolution exchange simulation. , 2005, Physical review letters.
[39] R. Jernigan,et al. Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.
[40] 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.
[41] Klaus Schulten,et al. Coarse grained protein-lipid model with application to lipoprotein particles. , 2006, The journal of physical chemistry. B.
[42] K C Holmes,et al. Normal modes as refinement parameters for the F-actin model. , 1995, Biophysical journal.
[43] H. Scheraga,et al. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. , 1976, Macromolecules.
[44] Wilma K Olson,et al. Normal-Mode Analysis of Circular DNA at the Base-Pair Level. 2. Large-Scale Configurational Transformation of a Naturally Curved Molecule. , 2005, Journal of chemical theory and computation.
[45] Gregory A Voth,et al. Multiscale simulation of transmembrane proteins. , 2007, Journal of structural biology.
[46] M. Levitt,et al. Computer simulation of protein folding , 1975, Nature.
[47] 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.
[48] O. Farago. “Water-free” computer model for fluid bilayer membranes , 2003, cond-mat/0304203.
[49] R. Jernigan,et al. Global ribosome motions revealed with elastic network model. , 2004, Journal of structural biology.
[50] R. Jernigan,et al. Structure-derived potentials and protein simulations. , 1996, Current opinion in structural biology.
[51] J. Onuchic,et al. Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.
[52] J. Berg,et al. Molecular dynamics simulations of biomolecules , 2002, Nature Structural Biology.
[53] Shoji Takada,et al. Optimizing physical energy functions for protein folding , 2003, Proteins.
[54] Gregory A Voth,et al. Multiscale coarse-graining and structural correlations: connections to liquid-state theory. , 2007, The journal of physical chemistry. B.
[55] Alexander P. Lyubartsev,et al. Multiscale modeling of lipids and lipid bilayers , 2005, European Biophysics Journal.
[56] N. Go. Theoretical studies of protein folding. , 1983, Annual review of biophysics and bioengineering.
[57] F. Tama,et al. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. , 2004, Journal of molecular biology.
[58] Charles L. Brooks,et al. The 13 Å Structure of a Chaperonin GroEL–Protein Substrate Complex by Cryo-electron Microscopy , 2005 .
[59] Haiyan Liu,et al. Molecular dynamics simulations of peptides and proteins with amplified collective motions. , 2003, Biophysical journal.
[60] T. Schlick,et al. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[61] Gregory A Voth,et al. Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[62] Tirion,et al. Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.
[63] Cecilia Clementi,et al. Minimalist protein model as a diagnostic tool for misfolding and aggregation. , 2006, Journal of molecular biology.
[64] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[65] Cezary Czaplewski,et al. Protein structure prediction with the UNRES force‐field using Replica‐Exchange Monte Carlo‐with‐Minimization; Comparison with MCM, CSA, and CFMC , 2005, J. Comput. Chem..
[66] M. Sippl. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. , 1990, Journal of molecular biology.
[67] Scott Brown,et al. Coarse-grained sequences for protein folding and design , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[68] Robert L Jernigan,et al. Loop motions of triosephosphate isomerase observed with elastic networks. , 2006, Biochemistry.
[69] E. Domany,et al. Pairwise contact potentials are unsuitable for protein folding , 1998 .
[70] Grace Brannigan,et al. Solvent-free simulations of fluid membrane bilayers. , 2004, The Journal of chemical physics.
[71] Holger Gohlke,et al. A natural coarse graining for simulating large biomolecular motion. , 2006, Biophysical journal.
[72] Gregory A Voth,et al. Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. , 2006, Biophysical journal.
[73] M. Levitt. A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.
[74] Stephen C Harvey,et al. Structural and thermodynamic principles of viral packaging. , 2007, Structure.
[75] Reinhard Lipowsky,et al. Computer simulations of bilayer membranes - self-assembly and interfacial tension. , 1998 .
[76] R. C. Reeder,et al. A Coarse Grain Model for Phospholipid Simulations , 2001 .
[77] D. Thirumalai,et al. Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures , 2003, physics/0302009.
[78] H. Stanley,et al. Discrete molecular dynamics simulations of peptide aggregation. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[79] K. Schulten,et al. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[80] Frank L. H. Brown,et al. Implicit solvent simulation models for biomembranes , 2005, European Biophysics Journal.