Learning To Fold Proteins Using Energy Landscape Theory

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

(2013) Mary A. Rohrdanz et al.   Annual Review of Physical Chemistry

Transthyretin as both a Sensor and a Scavenger of β-Amyloid Oligomers

(2013) Dennis T. Yang et al.   BIOCHEMISTRY

Funneling and frustration in the energy landscapes of some designed and simplified proteins

(2013) Ha H. Truong et al.   JOURNAL OF CHEMICAL PHYSICS

Spatial ranges of driving forces are a key determinant of protein folding cooperativity and rate diversity

(2013) Hüseyin Kaya et al.   PHYSICAL REVIEW E

Frustration in the energy landscapes of multidomain protein misfolding

(2013) W. Zheng 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

Free energy landscapes for initiation and branching of protein aggregation

(2013) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

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

The toxic Aβ oligomer and Alzheimer's disease: an emperor in need of clothes

(2012) Iryna Benilova et al.   NATURE NEUROSCIENCE

Discrete Kinetic Models from Funneled Energy Landscape Simulations

(2012) Nicholas P. Schafer et al.   PLoS One

Chemical physics of protein folding

(2012) P. G. Wolynes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predictive energy landscapes for protein-protein association

(2012) W. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Theoretical and Computational Protein Design

(2011) Ilan Samish et al.   Annual Review of Physical Chemistry

CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

(2011) Hiroo Kenzaki et al.   Journal of Chemical Theory and Computation

Prediction of Native-State Hydrogen Exchange from Perfectly Funneled Energy Landscapes

(2011) Patricio O. Craig et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

(2011) Stuart A. Sievers et al.   NATURE

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins

(2011) Wenfei Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Algorithm discovery by protein folding game players

(2011) F. Khatib et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

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

Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations

(2010)   BULLETIN OF THE KOREAN CHEMICAL SOCIETY

Protein structure prediction: Do hydrogen bonding and water-mediated interactions suffice?

(2010) Vanessa Oklejas et al.   METHODS

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

Entropic mechanism of large fluctuation in allosteric transition

(2010) Kazuhito Itoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying the amylome, proteins capable of forming amyloid-like fibrils

(2010) Lukasz Goldschmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Self-consistently optimized statistical mechanical energy functions for sequence structure alignment

(2010) K. K. Koretke et al.   PROTEIN SCIENCE

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

(2009) Zhuqing Zhang et al.   BIOPHYSICAL JOURNAL

Biophysical characterization of intrinsically disordered proteins

(2009) David Eliezer   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM: The biomolecular simulation program

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

The Molecular Origin of Like-Charge Arginine−Arginine Pairing in Water

(2009) Jiří Vondrášek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Electrostatic effects on funneled landscapes and structural diversity in denatured protein ensembles

(2009) Patrick Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Restriction versus guidance in protein structure prediction

(2009) J. A. Hegler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins

(2009) D. Nettels et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein structure prediction using basin-hopping

(2008) Michael C. Prentiss et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

Variationally Determined Free Energy Profiles for Structural Models of Proteins:  Characteristic Temperatures for Folding and Trapping†

(2008) Tongye Shen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Problem Solved* (*sort of)

(2008) R. F. Service   SCIENCE

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

(2007) Cecilia Clementi   CURRENT OPINION IN STRUCTURAL BIOLOGY