A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent

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

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spatial Decomposition of Solvation Free Energy Based on the 3D Integral Equation Theory of Molecular Liquid: Application to Miniproteins

(2010) Takeshi Yamazaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Relative entropy as a universal metric for multiscale errors

(2010) Aviel Chaimovich et al.   PHYSICAL REVIEW E

Three-dielectric-layer hybrid solvation model with spheroidal cavities in biomolecular simulations

(2010) Changfeng Xue et al.   PHYSICAL REVIEW E

Protein folded states are kinetic hubs

(2010) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models

(2009) Shina C. L. Kamerlin et al.   CHEMPHYSCHEM

Image Charge Methods for a Three-Dielectric-Layer Hybrid Solvation Model of Biomolecules

(2009) Peihua Qin et al.   Communications in Computational Physics

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

(2009) Vinod Krishna 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

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

(2009) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

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

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

Beyond the Poisson-Boltzmann Model: Modeling Biomolecule-Water and Water-Water Interactions

(2009) Patrice Koehl et al.   PHYSICAL REVIEW LETTERS

Potential for Modulation of the Hydrophobic Effect Inside Chaperonins

(2008) Jeremy L. England et al.   BIOPHYSICAL JOURNAL

Rattling the cage: computational models of chaperonin-mediated protein folding

(2008) Jeremy England 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

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations

(2008) Giuseppe Brancato et al.   JOURNAL OF CHEMICAL PHYSICS

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

(2008) Yuqing Deng 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

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area

(2008) Paul Labute   JOURNAL OF COMPUTATIONAL CHEMISTRY

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

(2008) Andreas Vitalis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Application of Mean Field Boundary Potentials in Simulations of Lipid Vesicles

(2008) H. Jelger Risselada et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond

(2007) Jayendran C. Rasaiah et al.   Annual Review of Physical Chemistry