A pH-dependent coarse-grained model for peptides

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Simple model for the simulation of peptide folding and aggregation with different sequences

(2012) Marta Enciso et al.   JOURNAL OF CHEMICAL PHYSICS

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

(2012) Stefano Piana et al.   PLoS One

Systematic coarse-graining methods for soft matter simulations – a review

(2012) Emiliano Brini et al.   Soft Matter

Coarse-grained models for protein aggregation

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

Locality and Fluctuations: Trends in Imidazolium-Based Ionic Liquids and Beyond

(2011) Katharina Wendler et al.   Journal of Chemical Theory and Computation

Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties

(2011) Arieh Warshel et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

pH replica-exchange method based on discrete protonation states

(2011) Satoru G. Itoh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein aggregation—Pathways and influencing factors

(2010) Wei Wang et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

A refined hydrogen bond potential for flexible protein models

(2010) Marta Enciso et al.   JOURNAL OF CHEMICAL PHYSICS

Selection of representative protein data sets

(2010) Uwe Hobohm et al.   PROTEIN SCIENCE

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

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

Self-assembly of protein amyloids: A competition between amorphous and ordered aggregation

(2009) Chiu Fan Lee   PHYSICAL REVIEW E

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

(2009) Benjamin M. Messer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Recent advances in implicit solvent-based methods for biomolecular simulations

(2008) Jianhan Chen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Protein aggregation: Pathways, induction factors and analysis

(2008) Hanns-Christian Mahler et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Coarse-Graining in Interaction Space:  A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials

(2008) Sergei Izvekov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane

(2008) Igor Vorobyov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Acidic range titration of HEWL using a constant-pH molecular dynamics method

(2008) Miguel Machuqueiro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2008) Christine Peter et al.   Soft Matter

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry