As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

Probing the structural dynamics of proteins and nucleic acids with optical tweezers

(2015) Dustin B Ritchie et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

(2015) Wenjun Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

Protein Transfer Free Energy Obeys Entropy-Enthalpy Compensation

(2015) Eric A. Mills et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamics of protein destabilization in live cells

(2015) Jens Danielsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconstructing Folding Energy Landscapes by Single-Molecule Force Spectroscopy

(2014) Michael T. Woodside et al.   Annual Review of Biophysics

Connecting Thermal and Mechanical Protein (Un)folding Landscapes

(2014) Li Sun et al.   BIOPHYSICAL JOURNAL

High-speed atomic force microscopy: Imaging and force spectroscopy

(2014) Frédéric Eghiaian et al.   FEBS LETTERS

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Molecular determinants of drug–receptor binding kinetics

(2013) Albert C. Pan et al.   DRUG DISCOVERY TODAY

A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain

(2013) Maksim Kouza et al.   JOURNAL OF CHEMICAL PHYSICS

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global structural motions from the strain of a single hydrogen bond

(2013) J. Danielsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOD1 exhibits allosteric frustration to facilitate metal binding affinity

(2013) A. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Native contacts determine protein folding mechanisms in atomistic simulations

(2013) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-level description of ubiquitin folding

(2013) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Force as a single molecule probe of multidimensional protein energy landscapes

(2012) Gabriel Žoldák et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Why and how does native topology dictate the folding speed of a protein?

(2012) Mark Rustad et al.   JOURNAL OF CHEMICAL PHYSICS

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

(2012) Aram Davtyan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Cutting Off Functional Loops from Homodimeric Enzyme Superoxide Dismutase 1 (SOD1) Leaves Monomeric β-Barrels

(2011) Jens Danielsson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

(2010) Jeffrey K. Noel et al.   NUCLEIC ACIDS RESEARCH

Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins

(2010) Z. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into protein folding mechanisms from large scale analysis of mutational effects

(2010) A. N. Naganathan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein folding simulations: From coarse-grained model to all-atom model

(2009) Jian Zhang et al.   IUBMB LIFE

Protein mechanical unfolding: Importance of non-native interactions

(2009) Maksim Kouza et al.   JOURNAL OF CHEMICAL PHYSICS

Coordinate-dependent diffusion in protein folding

(2009) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-Native Interactions Are Critical for Mechanical Strength in PKD Domains

(2009) Julia R. Forman et al.   STRUCTURE

Recent Advances in Optical Tweezers

(2008) Jeffrey R. Moffitt et al.   Annual Review of Biochemistry

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

An analytical study of the interplay between geometrical and energetic effects in protein folding

(2008) Yoko Suzuki et al.   JOURNAL OF CHEMICAL PHYSICS

The “Hot-Solvent/Cold-Solute” Problem Revisited

(2008) M. Lingenheil et al.   Journal of Chemical Theory and Computation

Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats

(2008) Amit Mor et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments

(2008) O. K. Dudko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY