Multiscale Coarse-Graining of the Protein Energy Landscape

A Complete Thermodynamic Characterization of Electrostatic and Hydrophobic Associations in the Temperature Range 0 to 100 °C from Explicit-Solvent Molecular Dynamics Simulations

(2010) Shun Zhu et al.   Journal of Chemical Theory and Computation

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining

(2010) Lanyuan Lu et al.   Journal of Chemical Theory and Computation

A Coarse-Grained Model Based on Morse Potential for Water andn-Alkanes

(2010) See-Wing Chiu et al.   Journal of Chemical Theory and Computation

Noncooperative Folding of Subdomains in Adenylate Kinase†

(2009) Louise Rundqvist et al.   BIOCHEMISTRY

A Free-Energy Approach for All-Atom Protein Simulation

(2009) Abhinav Verma et al.   BIOPHYSICAL JOURNAL

Force Field Bias in Protein Folding Simulations

(2009) Peter L. Freddolino et al.   BIOPHYSICAL JOURNAL

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

(2009) Marcos R. Betancourt et al.   JOURNAL OF CHEMICAL PHYSICS

Generic coarse-grained model for protein folding and aggregation

(2009) Tristan Bereau et al.   JOURNAL OF CHEMICAL PHYSICS

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

(2009) Russell DeVane et al.   Journal of Chemical Theory and Computation

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field

(2009) Yi He et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Desolvation Barrier Effects Are a Likely Contributor to the Remarkable Diversity in the Folding Rates of Small Proteins

(2009) Allison Ferguson et al.   JOURNAL OF MOLECULAR BIOLOGY

Energy Landscape of the Trpzip2 Peptide

(2009) Hugh Nymeyer   JOURNAL OF PHYSICAL CHEMISTRY B

Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining

(2009) Sergei Izvekov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic Coarse-graining of a Multicomponent Lipid Bilayer

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

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model

(2009) Alessandra Villa et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation

(2009) Alessandra Villa et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multiscale modeling of emergent materials: biological and soft matter

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

Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase

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

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

Generalized ensemble methods for de novo structure prediction

(2009) A. Shmygelska 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

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

A Bayesian statistics approach to multiscale coarse graining

(2008) Pu Liu 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

Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains

(2008) Wei Han et al.   Journal of Chemical Theory and Computation

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

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains

(2008) Mariusz Makowski 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

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

(2008) Hu-Jun Qian et al.   MACROMOLECULES

A temperature predictor for parallel tempering simulations

(2008) Alexandra Patriksson et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations

(2008) Srinivasaraghavan Kannan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Another look at the conditions for the extraction of protein knowledge-based potentials

(2008) Marcos R. Betancourt   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained models of protein folding: toy models or predictive tools?

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions

(2007) Jianhan Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE