Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Conservative and dissipative force field for simulation of coarse-grained alkane molecules: A bottom-up approach

(2014) Sébastien Trément et al.   JOURNAL OF CHEMICAL PHYSICS

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

(2014) Sergiy Markutsya et al.   JOURNAL OF CHEMICAL PHYSICS

The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation

(2014) Aram Davtyan et al.   Journal of Chemical Theory and Computation

Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems

(2014) Anand Srivastava et al.   Journal of Chemical Theory and Computation

Construction of dissipative particle dynamics models for complex fluids via the Mori–Zwanzig formulation

(2014) Zhen Li et al.   Soft Matter

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

Coarse-grain modelling of protein–protein interactions

(2013) Marc Baaden et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A test of systematic coarse-graining of molecular dynamics simulations: Transport properties

(2013) Chia-Chun Fu et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Coarse-grained molecular simulations of large biomolecules

(2012) Shoji Takada   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Hybrid Approach for Highly Coarse-Grained Lipid Bilayer Models

(2012) Anand Srivastava et al.   Journal of Chemical Theory and Computation

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

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

Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites

(2011) Juan J. de Pablo   Annual Review of Physical Chemistry

Obtaining fully dynamic coarse-grained models from MD

(2011) Pep Español et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

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

Colored-Noise Thermostats à la Carte

(2010) Michele Ceriotti et al.   Journal of Chemical Theory and Computation

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Modeling Kinetics of Subcellular Disposition of Chemicals

(2009) Stefan Balaz   CHEMICAL REVIEWS

Mori–Zwanzig formalism as a practical computational tool

(2009) Carmen Hijón et al.   FARADAY DISCUSSIONS

Systematic Coarse-graining of a Multicomponent Lipid Bilayer

(2009) Lanyuan Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effective control of the transport coefficients of a coarse-grained liquid and polymer models using the dissipative particle dynamics and Lowe–Andersen equations of motion

(2009) Hu-Jun Qian et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multiscale modeling of emergent materials: biological and soft matter

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

Nuclear Quantum Effects in Solids Using a Colored-Noise Thermostat

(2009) Michele Ceriotti et al.   PHYSICAL REVIEW LETTERS

Langevin Equation with Colored Noise for Constant-Temperature Molecular Dynamics Simulations

(2009) Michele Ceriotti et al.   PHYSICAL REVIEW LETTERS

Computational techniques for efficient conformational sampling of proteins

(2008) Adam Liwo et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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