Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange
暂无分享,去创建一个
[1] Alexander D. MacKerell,et al. Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide. , 2014, Biophysical journal.
[2] Michael Feig,et al. Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association , 2014, Journal of chemical theory and computation.
[3] Luís M. S. Loura,et al. How to tackle the issues in free energy simulations of long amphiphiles interacting with lipid membranes: convergence and local membrane deformations. , 2014, The journal of physical chemistry. B.
[4] Tristan Bereau,et al. More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization. , 2014, The Journal of chemical physics.
[5] Marc Baaden,et al. Coarse-grain modelling of protein-protein interactions. , 2013, Current opinion in structural biology.
[6] Yuji Sugita,et al. Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems. , 2013, Journal of chemical theory and computation.
[7] W G Noid,et al. Perspective: Coarse-grained models for biomolecular systems. , 2013, The Journal of chemical physics.
[8] Helgi I Ingólfsson,et al. The power of coarse graining in biomolecular simulations , 2013, Wiley interdisciplinary reviews. Computational molecular science.
[9] Régis Pomès,et al. Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. , 2013, Journal of chemical theory and computation.
[10] Christoph Globisch,et al. Optimization of an Elastic Network Augmented Coarse Grained Model to Study CCMV Capsid Deformation , 2013, PloS one.
[11] Vytautas Gapsys,et al. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations. , 2012, Journal of chemical theory and computation.
[12] Tristan Bereau,et al. Coarse-Grained and Atomistic Simulations of the Salt-Stable Cowpea Chlorotic Mottle Virus (SS-CCMV) Subunit 26-49: β-Barrel Stability of the Hexamer and Pentamer Geometries. , 2012, Journal of chemical theory and computation.
[13] Zun-Jing Wang,et al. A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations , 2012, The journal of physical chemistry. B.
[14] Karel Berka,et al. Convergence of Free Energy Profile of Coumarin in Lipid Bilayer , 2012, Journal of chemical theory and computation.
[15] Yun-Dong Wu,et al. Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix-Helix Association. , 2012, Journal of chemical theory and computation.
[16] W F Drew Bennett,et al. Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers. , 2011, Journal of chemical theory and computation.
[17] Tristan Bereau,et al. Structural basis of folding cooperativity in model proteins: insights from a microcanonical perspective. , 2011, Biophysical journal.
[18] K. Lindorff-Larsen,et al. How robust are protein folding simulations with respect to force field parameterization? , 2011, Biophysical journal.
[19] Klaus Schulten,et al. Challenges in protein-folding simulations , 2010 .
[20] D. Tieleman,et al. Interpretation of 2H-NMR experiments on the orientation of the transmembrane helix WALP23 by computer simulations. , 2010, Biophysical journal.
[21] M. Bachmann,et al. Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity , 2010, Journal of the American Chemical Society.
[22] M. Deserno,et al. Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field , 2010, New journal of physics.
[23] M. Deserno,et al. A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations , 2010, The Journal of Physical Chemistry. B.
[24] Wonpil Im,et al. Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation. , 2010, Biophysical journal.
[25] Benoît Roux,et al. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. , 2010, Journal of chemical theory and computation.
[26] A. Holt,et al. Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide. , 2010, Biophysical journal.
[27] Jeremy C. Smith,et al. Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. , 2010, Journal of the American Chemical Society.
[28] Helgi I. Ingólfsson,et al. Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes , 2010, Journal of The Royal Society Interface.
[29] J. Conboy,et al. Phospholipid flip-flop modulated by transmembrane peptides WALP and melittin. , 2009, Journal of structural biology.
[30] Xavier Periole,et al. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. , 2009, Journal of chemical theory and computation.
[31] Jeremy C. Smith,et al. Peptide Partitioning and Folding into Lipid Bilayers. , 2009, Journal of chemical theory and computation.
[32] Peter L. Freddolino,et al. Force field bias in protein folding simulations. , 2009, Biophysical journal.
[33] Y. Mu. Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange. , 2009, The Journal of chemical physics.
[34] Tristan Bereau,et al. Generic coarse-grained model for protein folding and aggregation. , 2009, The Journal of chemical physics.
[35] M. Ulmschneider,et al. Folding Peptides into Lipid Bilayer Membranes. , 2008, Journal of chemical theory and computation.
[36] W F Drew Bennett,et al. Distribution of amino acids in a lipid bilayer from computer simulations. , 2008, Biophysical journal.
[37] R. Larson,et al. The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.
[38] Alan Grossfield,et al. Convergence of molecular dynamics simulations of membrane proteins , 2007, Proteins.
[39] Ruhong Zhou,et al. Hydrophobic aided replica exchange: an efficient algorithm for protein folding in explicit solvent. , 2006, The journal of physical chemistry. B.
[40] Hans-Jörg Limbach,et al. ESPResSo - an extensible simulation package for research on soft matter systems , 2006, Comput. Phys. Commun..
[41] I. Tavernelli,et al. A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling. , 2006, Journal of chemical theory and computation.
[42] B. Berne,et al. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[43] C. Brooks,et al. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[44] Berend Smit,et al. Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. , 2005, Biophysical journal.
[45] Edward Lyman,et al. Resolution exchange simulation. , 2005, Physical review letters.
[46] A. Garcia,et al. Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study. , 2004, Physical review letters.
[47] H. Nymeyer,et al. Folding is not required for bilayer insertion: Replica exchange simulations of an α‐helical peptide with an explicit lipid bilayer , 2004, Proteins.
[48] C. Brooks,et al. De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. , 2004, Journal of molecular biology.
[49] J. Killian,et al. Synthetic peptides as models for intrinsic membrane proteins , 2003, FEBS letters.
[50] Martin Caffrey,et al. Membrane protein crystallization. , 2003, Journal of structural biology.
[51] S. Opella,et al. Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints , 2003, Protein science : a publication of the Protein Society.
[52] Yuko Okamoto,et al. Replica-exchange Monte Carlo method for the isobaric isothermal ensemble , 2001 .
[53] B. Dünweg,et al. Parallel excluded volume tempering for polymer melts. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.
[54] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[55] B. Duenweg,et al. Optimized Constant Pressure Stochastic Dynamics , 1999, cond-mat/9903423.
[56] J. Killian,et al. Influence of lipid/peptide hydrophobic mismatch on the thickness of diacylphosphatidylcholine bilayers. A 2H NMR and ESR study using designed transmembrane alpha-helical peptides and gramicidin A. , 1998, Biochemistry.
[57] S. Opella,et al. fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix. , 1997, Journal of molecular biology.
[58] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[59] P. Argos,et al. Knowledge‐based protein secondary structure assignment , 1995, Proteins.
[60] A. Ben-Shaul,et al. A molecular model for lipid-protein interaction in membranes: the role of hydrophobic mismatch. , 1993, Biophysical journal.
[61] Wang,et al. Replica Monte Carlo simulation of spin glasses. , 1986, Physical review letters.
[62] M. Bloom,et al. Mattress model of lipid-protein interactions in membranes. , 1984, Biophysical journal.
[63] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.
[64] M. Feig,et al. Recent advances in transferable coarse-grained modeling of proteins. , 2014, Advances in protein chemistry and structural biology.
[65] T. Bereau. Unconstrained Structure Formation in Coarse-Grained Protein Simulations , 2011 .
[66] G. von Heijne. Introduction to theme "membrane protein folding and insertion". , 2011, Annual review of biochemistry.
[67] L. DeLucas. Membrane protein crystallization , 2009 .
[68] Finn Verner Jensen,et al. Bayesian networks , 1998, Data Mining and Knowledge Discovery Handbook.
[69] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..