The impact of resolution upon entropy and information in coarse-grained models

Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions

(2015) Joseph F. Rudzinski et al.   Journal of Chemical Theory and Computation

Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics

(2015) Sunhwan Jo et al.   Journal of Chemical Theory and Computation

Thermomechanically Consistent and Temperature Transferable Coarse-Graining of Atactic Polystyrene

(2015) David D. Hsu et al.   MACROMOLECULES

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

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

Challenge of Representing Entropy at Different Levels of Resolution in Molecular Simulation

(2014) Wei Huang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Investigation of Coarse-Grained Mappings via an Iterative Generalized Yvon–Born–Green Method

(2014) Joseph F. Rudzinski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A series of PDB-related databanks for everyday needs

(2014) Wouter G. Touw et al.   NUCLEIC ACIDS RESEARCH

Minimizing memory as an objective for coarse-graining

(2013) Nicholas Guttenberg 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

A pH-dependent coarse-grained model for peptides

(2013) Marta Enciso et al.   Soft Matter

Coarse-grained methods for polymeric materials: enthalpy- and entropy-driven models

(2013) Paola Carbone et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Coarse-graining of multiprotein assemblies

(2012) Marissa G Saunders et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems

(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

Chemically transferable coarse-grained potentials from conditional reversible work calculations

(2012) E. Brini et al.   JOURNAL OF CHEMICAL PHYSICS

Water-Driven Cavity–Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations

(2012) Riccardo Baron et al.   Journal of Chemical Theory and Computation

Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes

(2012) Anton V. Sinitskiy 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

Thermodynamic Consistency between Analytic Integral Equation Theory and Coarse-Grained Molecular Dynamics Simulations of Homopolymer Melts

(2012) J. McCarty et al.   MACROMOLECULES

Thermodynamic transferability of coarse-grained potentials for polymer–additive systems

(2012) Emiliano Brini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

On developing coarse-grained models for biomolecular simulation: a review

(2012) Sereina Riniker et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic coarse-graining methods for soft matter simulations – a review

(2012) Emiliano Brini et al.   Soft Matter

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

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

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Exploration of Transferability in Multiscale Coarse-Grained Peptide Models

(2011) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

(2011) Ozge Engin et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble

(2010) Avisek Das et al.   JOURNAL OF CHEMICAL PHYSICS

Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water

(2010) Alessandra Villa et al.   Journal of Chemical Theory and Computation

Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data

(2010) Zhiyong Zhang 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

Relative entropy as a universal metric for multiscale errors

(2010) Aviel Chaimovich et al.   PHYSICAL REVIEW E

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

(2010) Timothy R. Lezon et al.   PLoS Computational Biology

Defining Coarse-Grained Representations of Large Biomolecules and Biomolecular Complexes from Elastic Network Models

(2009) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins

(2009) Ivet Bahar et al.   CHEMICAL REVIEWS

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?

(2009) Han Wang et al.   EUROPEAN PHYSICAL JOURNAL E

Multiscale simulation of soft matter systems

(2009) Christine Peter et al.   FARADAY DISCUSSIONS

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

(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

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl

(2009) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mesoscopic Membrane Physics: Concepts, Simulations, and Selected Applications

(2009) Markus Deserno   MACROMOLECULAR RAPID COMMUNICATIONS

Toy amphiphiles on the computer: What can we learn from generic models?

(2009) Friederike Schmid   MACROMOLECULAR RAPID COMMUNICATIONS

Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy

(2009) Aviel Chaimovich et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effective force coarse-graining

(2009) Yanting Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multiscale modeling of emergent materials: biological and soft matter

(2009) Teemu Murtola et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules

(2008) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

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

Temperature-Transferable Coarse-Grained Potentials for Ethylbenzene, Polystyrene, and Their Mixtures

(2008) Hu-Jun Qian et al.   MACROMOLECULES

Spectral Coarse Graining and Synchronization in Oscillator Networks

(2008) David Gfeller et al.   PHYSICAL REVIEW LETTERS