Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

Residue-Specific α-Helix Propensities from Molecular Simulation

(2012) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Trigger Factor Slows Co-translational Folding through Kinetic Trapping while Sterically Protecting the Nascent Chain from Aberrant Cytosolic Interactions

(2012) Edward P. O’Brien et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation

(2012) Bin Zhang et al.   Cell Reports

METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations

(2011) Xevi Biarnés et al.   COMPUTER PHYSICS COMMUNICATIONS

Coarse-grained models for protein aggregation

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

Coarse-grained model for protein folding based on structural profiles

(2011) Katrin Wolff et al.   PHYSICAL REVIEW E

A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding

(2011) Ivan Coluzza   PLoS One

Phase Diagram ofα-Helical andβ-Sheet Forming Peptides

(2010) Stefan Auer et al.   PHYSICAL REVIEW LETTERS

Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

(2010) Marcos R. Betancourt et al.   PROTEIN SCIENCE

Exploring the Universe of Protein Structures beyond the Protein Data Bank

(2010) Pilar Cossio et al.   PLoS Computational Biology

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics

(2009) Weihua Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Converging concepts of protein folding in vitro and in vivo

(2009) F Ulrich Hartl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Thermodynamics of tubelike flexible polymers

(2009) Thomas Vogel et al.   PHYSICAL REVIEW E

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation

(2009) Stefan Auer et al.   PLoS Computational Biology

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

(2009) Fabrizio Marinelli et al.   PLoS Computational Biology

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

Emergence of secondary motifs in tubelike polymers in a solvent

(2008) Chiara Poletto et al.   PHYSICAL REVIEW E

Self-Templated Nucleation in Peptide and Protein Aggregation

(2008) Stefan Auer et al.   PHYSICAL REVIEW LETTERS

A Generic Mechanism of Emergence of Amyloid Protofilaments from Disordered Oligomeric Aggregates

(2008) Stefan Auer et al.   PLoS Computational Biology

Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the α-helix

(2003) Bosco K. Ho et al.   PROTEIN SCIENCE