Minimalist models for proteins: a comparative analysis

Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds

(2010) Tap Ha-Duong   Journal of Chemical Theory and Computation

Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

(2010) Marcos R. Betancourt et al.   PROTEIN SCIENCE

Multiscale Modeling of Proteins

(2009) Valentina Tozzini   ACCOUNTS OF CHEMICAL RESEARCH

The structural dynamics of macromolecular processes

(2009) Daniel Russel et al.   CURRENT OPINION IN CELL BIOLOGY

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

A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements

(2009) Davide Alemani et al.   Journal of Chemical Theory and Computation

Effective force coarse-graining

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

A force field for virtual atom molecular mechanics of proteins

(2009) A. Korkut et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

(2009) Peter Májek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition

(2009) Armida Di Fenza et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

(2008) Edward Lyman et al.   BIOPHYSICAL JOURNAL

Multiscale methods for macromolecular simulations

(2008) Paul Sherwood 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

The MARTINI Coarse-Grained Force Field: Extension to Proteins

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

Coarse-grained force field for the nucleosome from self-consistent multiscaling

(2008) Karine Voltz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Peptide Folding Using Multiscale Coarse-Grained Models

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

Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

(2008) Patrick M. Buck et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE