A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Molecular Insights into Diphenylalanine Nanotube Assembly: All-Atom Simulations of Oligomerization

(2013) Joohyun Jeon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes

(2012) Cong Guo et al.   ACS Nano

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

(2012) Olga Bezkorovaynaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions

(2012) Biswaroop Mukherjee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

De novo designed peptides for biological applications

(2011) Aimee L. Boyle et al.   CHEMICAL SOCIETY REVIEWS

Materials from peptide assembly: towards the treatment of cancer and transmittable disease

(2011) Monica C Branco et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Coarse-grained models for protein aggregation

(2011) Chun Wu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions

(2011) Jia-Wei Shen et al.   Journal of Chemical Theory and Computation

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

Conditional reversible work method for molecular coarse graining applications

(2011) Emiliano Brini et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Coarse Graining of 4-Cyano-4′-pentylbiphenyl

(2010) Grigorios Megariotis et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

The multiscale coarse-graining method: Assessing its accuracy and introducing density dependent coarse-grain potentials

(2010) Sergei Izvekov et al.   JOURNAL OF CHEMICAL PHYSICS

Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water

(2010) Alessandra Villa et al.   Journal of Chemical Theory and Computation

Driving Forces for Adsorption of Amphiphilic Peptides to the Air−Water Interface

(2010) Ozge Engin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides

(2010) Martin B. Ulmschneider et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

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

(2009) Alexander Lyubartsev et al.   FARADAY DISCUSSIONS

Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer

(2009) Teemu Murtola et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains

(2009) Erik C. Allen 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

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

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

Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl

(2009) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2009) Christine Peter et al.   Soft Matter

Hydrogel Scaffolds of Amphiphilic and Acidicβ-Sheet Peptides

(2008) Hanna Rapaport et al.   ADVANCED FUNCTIONAL MATERIALS

Efficient prediction of thermodynamic properties of quadrupolar fluids from simulation of a coarse-grained model: The case of carbon dioxide

(2008) B. M. Mognetti 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

Water Modeled As an Intermediate Element between Carbon and Silicon†

(2008) Valeria Molinero et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2008) Christine Peter et al.   Soft Matter