Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

(2011) Ozge Engin et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane

(2011) Victor Rühle et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Role of Protein Interactions in Defining HIV-1 Viral Capsid Shape and Stability: A Coarse-Grained Analysis

(2010) Vinod Krishna et al.   BIOPHYSICAL JOURNAL

Molecular and Nanostructural Mechanisms of Deformation, Strength and Toughness of Spider Silk Fibrils

(2010) Andrea Nova et al.   NANO LETTERS

Recovering physical potentials from a model protein databank

(2010) J. W. Mullinax et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

(2009) Alexey Savelyev et al.   BIOPHYSICAL JOURNAL

Mechanical Response of Silk Crystalline Units from Force-Distribution Analysis

(2009) Senbo Xiao et al.   BIOPHYSICAL JOURNAL

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?

(2009) Han Wang et al.   EUROPEAN PHYSICAL JOURNAL E

A simple coarse-grained model for self-assembling silk-like protein fibers

(2009) Marieke Schor et al.   FARADAY DISCUSSIONS

Systematic coarse-graining of molecular models by the Newton inversion method

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

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

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

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

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

Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities

(2009) Dominik Fritz et al.   MACROMOLECULES

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

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

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

(2009) Christine Peter et al.   Soft Matter

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

Knowledge-Based Potential for the Polypeptide Backbone

(2008) Marcos R. Betancourt   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Folding Using Multiscale Coarse-Grained Models

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

Replica exchange simulations of transient encounter complexes in protein-protein association

(2008) Y. C. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE

Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal

(2008) Christine Peter et al.   Soft Matter

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

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY