Reduced atomic pair-interaction design (RAPID) model for simulations of proteins

Length-Dependent Aggregation of Uninterrupted Polyalanine Peptides

(2011) Joseph P. Bernacki et al.   BIOCHEMISTRY

Spontaneous Formation of Twisted Aβ16-22 Fibrils in Large-Scale Molecular-Dynamics Simulations

(2011) Mookyung Cheon et al.   BIOPHYSICAL JOURNAL

Effects of surface interactions on peptide aggregate morphology

(2011) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

An improved coarse-grained model of solvation and the hydrophobic effect

(2011) Patrick Varilly et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations

(2011) Andrij Baumketner et al.   PROTEIN SCIENCE

Mapping Conformational Ensembles of Aβ Oligomers in Molecular Dynamics Simulations

(2010) Seongwon Kim et al.   BIOPHYSICAL JOURNAL

Coarse-grained, density dependent implicit solvent model reliably reproduces behavior of a model surfactant system

(2009) Erik C. Allen et al.   JOURNAL OF CHEMICAL PHYSICS

Effect of β-sheet propensity on peptide aggregation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

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

Demixing Transition of the Aqueous Solution of Amyloidogenic Peptides: A REMD Simulation Study

(2009) Gurpreet Singh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Solvent-Free Lipid Bilayer Model Using Multiscale Coarse-Graining

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

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best 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

The Protein Folding Problem

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

Biomolecular simulation: historical picture and future perspectives

(2008) Wilfred F. van Gunsteren et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

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

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

Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment

(2008) Da-Wei Li et al.   PLoS Computational Biology

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

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

Spontaneous β-barrel formation: An all-atom Monte Carlo study of Aβ16–22 oligomerization

(2007) Anders Irbäck et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS