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

How determinant is N-terminal to C-terminal coupling for protein folding?

(2015) Heinrich Krobath et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

All-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex

(2014) Wenjun Zheng   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior

(2014) Sílvia G. Estácio et al.   PLoS Computational Biology

Modulation of a Protein Free-Energy Landscape by Circular Permutation

(2013) Gaël Radou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Identification of a Conserved Aggregation-Prone Intermediate State in the Folding Pathways of Spc-SH3 Amyloidogenic Variants

(2012) H. Krobath et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of an Intermediate State in Protein Folding and Aggregation

(2012) P. Neudecker et al.   SCIENCE

Accurate Flexible Fitting of High-Resolution Protein Structures into Cryo-Electron Microscopy Maps Using Coarse-Grained Pseudo-Energy Minimization

(2011) Wenjun Zheng   BIOPHYSICAL JOURNAL

Accurate Flexible Fitting of High-Resolution Protein Structures to Small-Angle X-Ray Scattering Data Using a Coarse-Grained Model with Implicit Hydration Shell

(2011) Wenjun Zheng et al.   BIOPHYSICAL JOURNAL

All-atom modeling of anisotropic atomic fluctuations in protein crystal structures

(2011) Jeffrey Hafner et al.   JOURNAL OF CHEMICAL PHYSICS

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

(2010) Wenjun Zheng   BIOPHYSICAL JOURNAL

The folding cooperativity of a protein is controlled by its chain topology

(2010) Elizabeth A. Shank et al.   NATURE

Destabilizing effect of proline substitutions in two helical regions of T4 lysozyme: Leucine 66 to proline and leucine 91 to proline

(2010) Terry M. Gray et al.   PROTEIN SCIENCE

Predicting order of conformational changes during protein conformational transitions using an interpolated elastic network model

(2010) Mustafa Tekpinar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Application of Elastic Network Models to Proteins in the Crystalline State

(2009) Demian Riccardi et al.   BIOPHYSICAL JOURNAL

The perspectives of studying multi-domain protein folding

(2009) J. Fitter   CELLULAR AND MOLECULAR LIFE SCIENCES

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein elastic network models and the ranges of cooperativity

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Unification of the Elastic Network Model and the Gaussian Network Model for Optimal Description of Protein Conformational Motions and Fluctuations

(2008) Wenjun Zheng   BIOPHYSICAL JOURNAL

Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: Evidence for a kinetic partitioning mechanism

(2008) Q. Peng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FACTS: Fast analytical continuum treatment of solvation

(2007) Urs Haberthür et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Predicting the order in which contacts are broken during single molecule protein stretching experiments

(2007) Joanna I. Sułkowska et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS