Evaluation of a fast implicit solvent model for molecular dynamics simulations (original) (raw)
A semi-implicit solvent model for the simulation of peptides and proteins
Daniel Borgis
Journal of Computational Chemistry, 2004
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Prediction of helical peptide folding in an implicit water by a new molecular dynamics scheme with generalized effective potential
Soonmin Jang
The Journal of Chemical Physics, 2002
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Simulations of the role of water in the protein-folding mechanism
Eric Sorin
Proceedings of the National Academy of Sciences, 2004
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Protein Structure and Dynamics in Nonaqueous Solvents: Insights from Molecular Dynamics Simulation Studies
Claudio Soares
Biophysical Journal, 2003
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Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations
Jens Kleinjung
Journal of Chemical Theory and Computation, 2012
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Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
Marcus Elstner
Proteins: Structure, Function, and Bioinformatics, 2003
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Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent
Giúp ViệcPhương Nam - Dịch Vụ Giúp Việc Gia Đình
Journal of the American Chemical Society, 2014
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Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding
Andrea Amadei
Proceedings of the National Academy of Sciences, 2007
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A Solvent Model for Simulations of Peptides in Bilayers. I. Membrane-Promoting α-Helix Formation
Roman Efremov
Biophysical Journal, 1999
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A Solvent Model for Simulations of Peptides in Bilayers. II. Membrane-Spanning α-Helices
Roman Efremov
Biophysical Journal, 1999
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Molecular Dynamics Simulations of Proteins and Peptides: From Folding to Drug Design
paul tavan
Current Protein & Peptide Science, 2008
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Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites
Flavia Autore
Methods in molecular biology (Clifton, N.J.)
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Improved generalized born solvent model parameters for protein simulations
Hai Nguyen
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Simplified models of protein folding exploiting the Lagrange radius of gyration of the hydrophobic component
Barry Robson
Parallel Computing, 2000
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Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water
Benoît Roux
1997
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Exploring Peptide–Solvent Interactions: A Computational Study
Nadia Elghobashi-Meinhardt
Molecules, 2018
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Effects of different water models as explicit solvent on folding of Human Prion Protein by Molecular Dynamic Simulation
Mohammad Reza Dayer
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Polarization effects on peptide conformations at water-membrane interface by molecular dynamics simulation
Amando Ito
Journal of Computational Chemistry, 1999
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Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model
Andrew Bordner
Journal of Computer-Aided Molecular Design, 2011
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A Molecular Dynamics Study of the Correlations between Solvent-Accessible Surface, Molecular Volume, and Folding State
Marco Antonio C Nascimento
The Journal of Physical Chemistry B, 2007
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Design and application of implicit solvent models in biomolecular simulations
Jens Kleinjung
Current Opinion in Structural Biology, 2014
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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a â-Hairpin Peptide
Chris T J C Ward
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CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
sandeep patel
Journal of Computational Chemistry, 2004
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β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water
Xiongwu Wu
Biophysical Journal, 2004
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Implicit solvation model and hydrophobicity scale for protein folding
David J E Callaway
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Reversible Peptide Folding in Solution by Molecular Dynamics Simulation
Xavier Daura
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Dominant Solvation Effects from the Primary Shell of Hydration Approximation for Molecular Dynamics Simulations
Benoit Roux
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Reversible peptide folding in solution by molecular dynamics simulation1
Xavier Daura
Journal of Molecular Biology, 1998
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Protonation States in Molecular Dynamics Simulations of Peptide Folding and Binding
Masha Niv
Current Pharmaceutical Design, 2013
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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide †
Ruhong Zhou
The Journal of Physical Chemistry B, 2004
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Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
Trevor Creamer
Biochemistry, 1997
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Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations
Amedeo Caflisch
The Journal of Physical Chemistry B, 2000
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A coarse-grained protein model in a water-like solvent
sumit sharma
Scientific reports, 2013
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