标题
A generalized-Yvon-Born-Green method for coarse-grained modeling
作者
关键词
European Physical Journal Special Topic, Pair Potential, Pair Distribution Function, Indirect Contribution, Structure Ensemble
出版物
European Physical Journal-Special Topics
Volume 224, Issue 12, Pages 2193-2216
出版商
Springer Nature
发表日期
2015-06-22
DOI
10.1140/epjst/e2015-02408-9
参考文献
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注意：仅列出部分参考文献，下载原文获取全部文献信息。- Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions
- (2015) Joseph F. Rudzinski et al. Journal of Chemical Theory and Computation
- An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale
- (2014) J. McCarty et al. JOURNAL OF CHEMICAL PHYSICS
- Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion
- (2014) Timothy C. Moore et al. JOURNAL OF CHEMICAL PHYSICS
- A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method
- (2014) Aymeric Naômé et al. Journal of Chemical Theory and Computation
- Coarse-Graining of TIP4P/2005, TIP4P-Ew, SPC/E, and TIP3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization
- (2014) Jibao Lu et al. Journal of Chemical Theory and Computation
- Investigation of Coarse-Grained Mappings via an Iterative Generalized Yvon–Born–Green Method
- (2014) Joseph F. Rudzinski et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Understanding shape entropy through local dense packing
- (2014) Greg van Anders et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Energy Functions in De Novo Protein Design: Current Challenges and Future Prospects
- (2013) Zhixiu Li et al. Annual Review of Biophysics
- Fitting coarse-grained distribution functions through an iterative force-matching method
- (2013) Lanyuan Lu et al. JOURNAL OF CHEMICAL PHYSICS
- Predicting the thermodynamics by using state-dependent interactions
- (2013) Giuseppe D'Adamo et al. JOURNAL OF CHEMICAL PHYSICS
- Perspective: Coarse-grained models for biomolecular systems
- (2013) W. G. Noid JOURNAL OF CHEMICAL PHYSICS
- Estimation of Interaction Potentials through the Configurational Temperature Formalism
- (2013) Martin Mechelke et al. Journal of Chemical Theory and Computation
- A pH-dependent coarse-grained model for peptides
- (2013) Marta Enciso et al. Soft Matter
- Engineering shape: the novel geometries of colloidal self-assembly
- (2013) Stefano Sacanna et al. Soft Matter
- Scaling behavior and local structure of ion aggregates in single-ion conductors
- (2013) Keran Lu et al. Soft Matter
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- (2012) Avisek Das et al. JOURNAL OF CHEMICAL PHYSICS
- A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties
- (2012) Chia-Chun Fu et al. JOURNAL OF CHEMICAL PHYSICS
- The multiscale coarse-graining method. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarse-grained force fields
- (2012) Avisek Das et al. JOURNAL OF CHEMICAL PHYSICS
- Structure-based coarse-graining in liquid slabs
- (2012) Mara Jochum et al. JOURNAL OF CHEMICAL PHYSICS
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- (2012) Avisek Das et al. JOURNAL OF CHEMICAL PHYSICS
- Chemically transferable coarse-grained potentials from conditional reversible work calculations
- (2012) E. Brini et al. JOURNAL OF CHEMICAL PHYSICS
- Coarse-Grained Potential Model for Structural Prediction of Confined Water
- (2012) S. Y. Mashayak et al. Journal of Chemical Theory and Computation
- The Role of Many-Body Correlations in Determining Potentials for Coarse-Grained Models of Equilibrium Structure
- (2012) Joseph F. Rudzinski et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly
- (2012) Scott P. Carmichael et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions
- (2012) Biswaroop Mukherjee et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Cation Coordination and Motion in a Poly(ethylene oxide)-Based Single Ion Conductor
- (2012) Kan-Ju Lin et al. MACROMOLECULES
- Thermodynamic transferability of coarse-grained potentials for polymer–additive systems
- (2012) Emiliano Brini et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Optical microscopy measurements of kT-scale colloidal interactions
- (2011) Michael A. Bevan et al. CURRENT OPINION IN COLLOID & INTERFACE SCIENCE
- Coarse-graining entropy, forces, and structures
- (2011) Joseph F. Rudzinski et al. JOURNAL OF CHEMICAL PHYSICS
- Towards an understanding of many-particle effects in hydrophobic association in methane solutions
- (2011) Sergei Izvekov JOURNAL OF CHEMICAL PHYSICS
- The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials
- (2011) Lanyuan Lu et al. JOURNAL OF CHEMICAL PHYSICS
- Coarse-graining errors and numerical optimization using a relative entropy framework
- (2011) Aviel Chaimovich et al. JOURNAL OF CHEMICAL PHYSICS
- Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining
- (2011) W.F. Drew Bennett et al. Journal of Chemical Theory and Computation
- Generalized-Yvon-Born-Green Model of Toluene
- (2011) Christopher R. Ellis et al. MACROMOLECULAR THEORY AND SIMULATIONS
- A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models
- (2011) Ozge Engin et al. MACROMOLECULAR THEORY AND SIMULATIONS
- Conditional reversible work method for molecular coarse graining applications
- (2011) Emiliano Brini et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Systematic Coarse Graining of 4-Cyano-4′-pentylbiphenyl
- (2010) Grigorios Megariotis et al. INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
- Reference state for the generalized Yvon–Born–Green theory: Application for coarse-grained model of hydrophobic hydration
- (2010) J. W. Mullinax et al. JOURNAL OF CHEMICAL PHYSICS
- A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
- (2010) Alex Morriss-Andrews et al. JOURNAL OF CHEMICAL PHYSICS
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- (2010) Luca Larini et al. JOURNAL OF CHEMICAL PHYSICS
- The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
- (2010) Avisek Das et al. JOURNAL OF CHEMICAL PHYSICS
- Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining
- (2010) Lanyuan Lu et al. Journal of Chemical Theory and Computation
- Temperature dependence of coarse-grained potentials for liquid hexane
- (2010) Karim Farah et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Chemically accurate coarse graining of double-stranded DNA
- (2010) A. Savelyev et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Recovering physical potentials from a model protein databank
- (2010) J. W. Mullinax et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology
- (2010) Timothy R. Lezon et al. PLoS Computational Biology
- Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA
- (2009) Alexey Savelyev et al. BIOPHYSICAL JOURNAL
- Systematic coarse-graining of molecular models by the Newton inversion method
- (2009) Alexander Lyubartsev et al. FARADAY DISCUSSIONS
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- (2009) Hyung Min Cho et al. JOURNAL OF CHEMICAL PHYSICS
- Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer
- (2009) Teemu Murtola et al. JOURNAL OF CHEMICAL PHYSICS
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- (2009) Vinod Krishna et al. JOURNAL OF CHEMICAL PHYSICS
- Extended ensemble approach for deriving transferable coarse-grained potentials
- (2009) J. W. Mullinax et al. JOURNAL OF CHEMICAL PHYSICS
- The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation
- (2009) Avisek Das et al. JOURNAL OF CHEMICAL PHYSICS
- Versatile Object-Oriented Toolkit for Coarse-Graining Applications
- (2009) Victor Rühle et al. Journal of Chemical Theory and Computation
- Multiscale Modeling of Coarse-Grained Macromolecular Liquids
- (2009) J. McCarty et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl
- (2009) Alexey Savelyev et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials
- (2009) J. W. Mullinax et al. Journal of Physical Chemistry C
- Generalized Yvon-Born-Green Theory for Molecular Systems
- (2009) J. W. Mullinax et al. PHYSICAL REVIEW LETTERS
- Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
- (2009) Emil Sobolewski et al. PROTEIN ENGINEERING DESIGN & SELECTION
- Inverse optimization techniques for targeted self-assembly
- (2009) Salvatore Torquato Soft Matter
- The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
- (2008) W. G. Noid et al. JOURNAL OF CHEMICAL PHYSICS
- The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
- (2008) W. G. Noid et al. JOURNAL OF CHEMICAL PHYSICS
- The relative entropy is fundamental to multiscale and inverse thermodynamic problems
- (2008) M. Scott Shell JOURNAL OF CHEMICAL PHYSICS
- Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane
- (2008) Igor Vorobyov et al. JOURNAL OF PHYSICAL CHEMISTRY B
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- (2008) Hu-Jun Qian et al. MACROMOLECULES
- Another look at the conditions for the extraction of protein knowledge-based potentials
- (2008) Marcos R. Betancourt PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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