α-helix to β-hairpin transition of human amylin monomer

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Aggregation of islet amyloid polypeptide: from physical chemistry to cell biology

(2012) Ping Cao et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains

(2012) Wei Han et al.   Journal of Chemical Theory and Computation

Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

(2012) Chris T. Middleton et al.   Nature Chemistry

Protein folding kinetics and thermodynamics from atomistic simulation

(2012) S. Piana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

Density of States–Based Molecular Simulations

(2012) Sadanand Singh et al.   Annual Review of Chemical and Biomolecular Engineering

Modulation of fibrillation of hIAPP core fragments by chemical modification of the peptide backbone

(2011) Maria Andreasen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Fibril Structure of Human Islet Amyloid Polypeptide

(2011) Sahar Bedrood et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

(2011) Paul S. Nerenberg et al.   Journal of Chemical Theory and Computation

Sensitivity of Amyloid Formation by Human Islet Amyloid Polypeptide to Mutations at Residue 20

(2011) Ping Cao et al.   JOURNAL OF MOLECULAR BIOLOGY

2DIR Spectroscopy of Human Amylin Fibrils Reflects Stable β-Sheet Structure

(2011) Lu Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Amyloid Formation Mechanism in Human IAPP: Dimers Have β-Strand Monomer−Monomer Interfaces

(2011) Nicholas F. Dupuis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Islet Amyloid Polypeptide, Islet Amyloid, and Diabetes Mellitus

(2011) Per Westermark et al.   PHYSIOLOGICAL REVIEWS

Microscopic events in  -hairpin folding from alternative unfolded ensembles

(2011) R. B. Best et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spectroscopic studies of protein folding: Linear and nonlinear methods

(2011) Arnaldo L. Serrano et al.   PROTEIN SCIENCE

GNNQQNY—Investigation of Early Steps during Amyloid Formation

(2010) Allam S. Reddy et al.   BIOPHYSICAL JOURNAL

Stable and Metastable States of Human Amylin in Solution

(2010) Allam S. Reddy et al.   BIOPHYSICAL JOURNAL

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

(2010) Robert B. Best et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

(2009) Robert A. Latour   Biointerphases

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

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Dynamic α-Helix Structure of Micelle-bound Human Amylin

(2009) Sharadrao M. Patil et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The stochastic separatrix and the reaction coordinate for complex systems

(2009) Dimitri Antoniou et al.   JOURNAL OF CHEMICAL PHYSICS

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

Amyloidogenic Propensities and Conformational Properties of ProIAPP and IAPP in the Presence of Lipid Bilayer Membranes

(2009) Suman Jha et al.   JOURNAL OF MOLECULAR BIOLOGY

Human Islet Amyloid Polypeptide Monomers Form Ordered β-hairpins: A Possible Direct Amyloidogenic Precursor

(2009) Nicholas F. Dupuis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Two-dimensional IR spectroscopy and isotope labeling defines the pathway of amyloid formation with residue-specific resolution

(2009) S.-H. Shim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Solution state structures of human pancreatic amylin and pramlintide

(2009) John R. Cort et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Amylin Proprotein Processing Generates Progressively More Amyloidogenic Peptides that Initially Sample the Helical State†

(2008) Isaac T. Yonemoto et al.   BIOCHEMISTRY

Folding of polyglutamine chains

(2008) Manan Chopra et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Principal Component Analysis for Protein Folding Dynamics

(2008) Gia G. Maisuradze et al.   JOURNAL OF MOLECULAR BIOLOGY

Early events in protein folding: Is there something more than hydrophobic burst?

(2008) Carlo Camilloni et al.   PROTEIN SCIENCE

Interaction of membrane-bound islet amyloid polypeptide with soluble and crystalline insulin

(2008) Jefferson D. Knight et al.   PROTEIN SCIENCE

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS