The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

(2015) Jessica Nasica-Labouze et al.   CHEMICAL REVIEWS

Introducing Protein Intrinsic Disorder

(2014) Johnny Habchi et al.   CHEMICAL REVIEWS

Temperature-dependent solvation modulates the dimensions of disordered proteins

(2014) R. Wuttke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Carnosine Inhibits Aβ42Aggregation by Perturbing the H-Bond Network in and around the Central Hydrophobic Cluster

(2013) Francesco Attanasio et al.   CHEMBIOCHEM

Stable conformation of full-length amyloid-β (1–42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

(2013) Akisumi Okamoto et al.   CHEMICAL PHYSICS LETTERS

Insights into Aβ Aggregation: A Molecular Dynamics Perspective

(2013) Joan-Emma Shea et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide

(2013) Maximillian Zhu et al.   JOURNAL OF CHEMICAL PHYSICS

Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

(2013) David J. Rosenman et al.   JOURNAL OF MOLECULAR BIOLOGY

Single-Molecule Spectroscopy of Cold Denaturation and the Temperature-Induced Collapse of Unfolded Proteins

(2013) Mikayel Aznauryan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A decade and a half of protein intrinsic disorder: Biology still waits for physics

(2013) Vladimir N. Uversky   PROTEIN SCIENCE

Describing sequence–ensemble relationships for intrinsically disordered proteins

(2012) Albert H. Mao et al.   BIOCHEMICAL JOURNAL

Effects of Familial Mutations on the Monomer Structure of Aβ42

(2012) Yu-Shan Lin et al.   BIOPHYSICAL JOURNAL

Structure of an Intermediate State in Protein Folding and Aggregation

(2012) P. Neudecker et al.   SCIENCE

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Intrinsically disordered proteins: a 10-year recap

(2012) Peter Tompa   TRENDS IN BIOCHEMICAL SCIENCES

A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations

(2012) Michael Knott et al.   PLoS Computational Biology

Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides

(2011) K. Aurelia Ball et al.   BIOCHEMISTRY

Compaction Properties of an Intrinsically Disordered Protein: Sic1 and Its Kinase-Inhibitor Domain

(2011) Stefania Brocca et al.   BIOPHYSICAL JOURNAL

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Constructing ensembles for intrinsically disordered proteins

(2011) Charles K Fisher et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

(2011) Sébastien Côté et al.   Journal of Chemical Theory and Computation

Understanding the structural ensembles of a highly extended disordered protein

(2011) Gary W. Daughdrill et al.   Molecular BioSystems

Are native proteins metastable?

(2011) D. Thirumalai et al.   Nature Chemistry

Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility

(2011) A. De Simone et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ensemble modeling of protein disordered states: Experimental restraint contributions and validation

(2011) Joseph A. Marsh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Understanding protein non-folding

(2010) Vladimir N. Uversky et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

(2010) Yang Shen et al.   JOURNAL OF BIOMOLECULAR NMR

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

(2010) Nikolaos G. Sgourakis et al.   JOURNAL OF MOLECULAR BIOLOGY

Protein Heat Capacity: An Anomaly that Maybe Never Was

(2010) Alan Cooper   Journal of Physical Chemistry Letters

Temperature-dependent structural changes in intrinsically disordered proteins: Formation of α-helices or loss of polyproline II?

(2010) Magnus Kjaergaard et al.   PROTEIN SCIENCE

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

A facile method for expression and purification of the Alzheimer’s disease-associated amyloid β-peptide

(2009) Dominic M. Walsh et al.   FEBS Journal

A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1

(2009) Fabio Pietrucci et al.   Journal of Chemical Theory and Computation

Determination of the Free Energy Landscape of α-Synuclein Using Spin Label Nuclear Magnetic Resonance Measurements

(2009) Jane R. Allison et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Quantitative Determination of the Conformational Properties of Partially Folded and Intrinsically Disordered Proteins Using NMR Dipolar Couplings

(2009) Malene Ringkjøbing Jensen et al.   STRUCTURE

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor

(2008) T. Mittag et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation

Charge states rather than propensity for β-structure determine enhanced fibrillogenesis in wild-type Alzheimer's β-amyloid peptide compared to E22Q Dutch mutant

(2002) Francesca Massi et al.   PROTEIN SCIENCE