Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

Native Topology of the Designed Protein Top7 is Not Conducive to Cooperative Folding

(2009) Zhuqing Zhang et al.   BIOPHYSICAL JOURNAL

The Protein Folding Problem

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

Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water

(2008) Jarek Juraszek et al.   BIOPHYSICAL JOURNAL

Coevolution of Function and the Folding Landscape: Correlation with Density of Native Contacts

(2008) Ronald D. Hills et al.   BIOPHYSICAL JOURNAL

Selection of Optimal Variants of Gō-Like Models of Proteins through Studies of Stretching

(2008) Joanna I. Sułkowska et al.   BIOPHYSICAL JOURNAL

Multiscale methods for macromolecular simulations

(2008) Paul Sherwood et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Folding mechanisms of individual β-hairpins in a Gō model of Pin1 WW domain by all-atom molecular dynamics simulations

(2008) Zhonglin Luo et al.   JOURNAL OF CHEMICAL PHYSICS

Simulations of the protein folding process using topology-based models depend on the experimental structure

(2008) Lidia Prieto et al.   JOURNAL OF CHEMICAL PHYSICS

Toward a Coarse-Grained Protein Model Coupled with a Coarse-Grained Solvent Model: Solvation Free Energies of Amino Acid Side Chains

(2008) Wei Han et al.   Journal of Chemical Theory and Computation

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Topology-based models and NMR structures in protein folding simulations

(2008) M. Fernanda Rey-Stolle et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Subdomain Competition, Cooperativity, and Topological Frustration in the Folding of CheY

(2008) Ronald D. Hills et al.   JOURNAL OF MOLECULAR BIOLOGY

Kinetic Traps in the Folding of βα-Repeat Proteins: CheY Initially Misfolds before Accessing the Native Conformation

(2008) Sagar V. Kathuria et al.   JOURNAL OF MOLECULAR BIOLOGY

Characterization of Protein Folding by Dominant Reaction Pathways

(2008) Pietro Faccioli   JOURNAL OF PHYSICAL CHEMISTRY B

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains

(2008) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crystallographic B-Factors Highlight Energetic Frustration in Aldolase Folding

(2008) Maithreyi K. Rao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptide Folding Using Multiscale Coarse-Grained Models

(2008) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crowding Effects on the Mechanical Stability and Unfolding Pathways of Ubiquitin

(2008) David L. Pincus et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Advillin Folding Takes Place on a Hypersurface of Small Dimensionality

(2008) Stefano Piana et al.   PHYSICAL REVIEW LETTERS

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

(2008) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crowded, cell-like environment induces shape changes in aspherical protein

(2008) D. Homouz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding

(2008) A. Zarrine-Afsar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extracting function from a  -trefoil folding motif

(2008) S. Gosavi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stabilizing effect of knots on proteins

(2008) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins

(2008) Carlos H. da Silveira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

Protofibril Assemblies of the Arctic, Dutch, and Flemish Mutants of the Alzheimer's Aβ1–40 Peptide

(2007) Nicolas Lux Fawzi et al.   BIOPHYSICAL JOURNAL

Microseconds Dynamics Simulations of the Outer-Membrane Protease T

(2007) Marilisa Neri et al.   BIOPHYSICAL JOURNAL

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

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE