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

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

Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

(2009) R. B. Pandey et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Systematic Coarse-graining of a Multicomponent Lipid Bilayer

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

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes

(2008) Kei Moritsugu et al.   BIOPHYSICAL JOURNAL

A polarizable coarse-grained water model for coarse-grained proteins simulations

(2008) Tap Ha-Duong et al.   CHEMICAL PHYSICS LETTERS

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 MARTINI Coarse-Grained Force Field: Extension to Proteins

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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Coarse-Graining Protein Structures With Local Multivariate Features from Molecular Dynamics

(2008) Zhiyong Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Folding Using Multiscale Coarse-Grained Models

(2008) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography

(2008) M. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA