Published in Wiley Interdiscip Rev Comput Mol Sci on May 01, 2014
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COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput (2014) 0.80
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Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J Chem Phys (2011) 1.24
Martini Coarse-Grained Force Field: Extension to Carbohydrates. J Chem Theory Comput (2009) 1.23
A coarse-grained protein force field for folding and structure prediction. Proteins (2007) 1.21
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A fast method for large-scale de novo peptide and miniprotein structure prediction. J Comput Chem (2010) 1.20
Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. J Phys Chem A (2010) 1.19
Zwitterionic lipid assemblies: molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B (2010) 1.19
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Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Sci Rep (2013) 1.14
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Multiscale modeling of emergent materials: biological and soft matter. Phys Chem Chem Phys (2009) 1.09
A systematic methodology for defining coarse-grained sites in large biomolecules. Biophys J (2008) 1.09
Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Sci Rep (2013) 1.05
A coarse-grained protein-protein potential derived from an all-atom force field. J Phys Chem B (2007) 1.05
Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys Chem Chem Phys (2011) 1.04
Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field. J Mol Biol (2010) 1.04
Sequence-dependent thermodynamics of a coarse-grained DNA model. J Chem Phys (2012) 1.04
Hybrid coarse-graining approach for lipid bilayers at large length and time scales. J Phys Chem B (2009) 1.02
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A coarse-grained molecular model for glycosaminoglycans: application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophys J (2005) 1.02
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Coarse-grained force field: general folding theory. Phys Chem Chem Phys (2011) 0.99
PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins (2010) 0.99
The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One (2011) 0.98
A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality. J Chem Phys (2010) 0.98
A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations. J Phys Chem B (2010) 0.98
Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers. J Chem Theory Comput (2006) 0.98
Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B (2010) 0.98
DNA nanotweezers studied with a coarse-grained model of DNA. Phys Rev Lett (2010) 0.98
Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations. J Phys Chem B (2013) 0.97
Martini Force Field Parameters for Glycolipids. J Chem Theory Comput (2013) 0.97
A quantitative coarse-grain model for lipid bilayers. J Phys Chem B (2007) 0.97
Coarse-graining errors and numerical optimization using a relative entropy framework. J Chem Phys (2011) 0.96
Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields. J Chem Theory Comput (2012) 0.96
Multiscale coarse-graining of monosaccharides. J Phys Chem B (2007) 0.95
A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics. J Chem Theory Comput (2010) 0.95
Systematic coarse-graining of a multicomponent lipid bilayer. J Phys Chem B (2009) 0.95
Multiscale characterization of protein conformational ensembles. Proteins (2009) 0.95
Comparative atomistic and coarse-grained study of water: what do we lose by coarse-graining? Eur Phys J E Soft Matter (2009) 0.93
Molecular dynamics with the United-residue force field: ab initio folding simulations of multichain proteins. J Phys Chem B (2007) 0.92
A Hybrid Approach for Highly Coarse-grained Lipid Bilayer Models. J Chem Theory Comput (2013) 0.92
HiRE-RNA: a high resolution coarse-grained energy model for RNA. J Phys Chem B (2010) 0.92
Computational simulations of the early steps of protein aggregation. Prion (2007) 0.92