Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

FTIR spectroscopic imaging of protein aggregation in living cells

(2013) Lisa M. Miller et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins

(2013) Rabia Sarroukh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Molecular Dynamics Simulations of Highly Crowded Amino Acid Solutions: Comparisons of Eight Different Force Field Combinations with Experiment and with Each Other

(2013) Casey T. Andrews et al.   Journal of Chemical Theory and Computation

Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions

(2013) Ryuhei Harada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

(2013) Christian Margreitter et al.   NUCLEIC ACIDS RESEARCH

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

(2013) Drazen Petrov et al.   PLoS Computational Biology

Optimizing Solute–Water van der Waals Interactions To Reproduce Solvation Free Energies

(2012) Paul S. Nerenberg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Dynamics of an Unfolded Protein Examined by Molecular Dynamics Simulation

(2012) Kresten Lindorff-Larsen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Crowding Affects Hydration Structure and Dynamics

(2012) Ryuhei Harada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

Multimolecule test-tube simulations of protein unfolding and aggregation

(2012) M. E. McCully et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Aggregation in Protein-Based Biotherapeutics: Computational Studies and Tools to Identify Aggregation-Prone Regions

(2011) Neeraj J. Agrawal et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Variable Interactions between Protein Crowders and Biomolecular Solutes Are Important in Understanding Cellular Crowding

(2011) Michael Feig et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Microscopic Analysis of Protein Oxidative Damage: Effect of Carbonylation on Structure, Dynamics, and Aggregability of Villin Headpiece

(2011) Drazen Petrov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy

(2011) Jean K. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular and supramolecular studies on polyglycine and poly-l-proline

(2011) Marina Lorusso et al.   Soft Matter

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

(2010) Adrian H Elcock   CURRENT OPINION IN STRUCTURAL BIOLOGY

Insulin dimer dissociation and unfolding revealed by amide I two-dimensional infrared spectroscopy

(2010) Ziad Ganim et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

Probing the Folding Transition State Structure of the Villin Headpiece Subdomain via Side Chain and Backbone Mutagenesis

(2009) Michelle R. Bunagan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational averaging in structural biology: issues, challenges and computational solutions

(2009) Daniela Kruschel et al.   Molecular BioSystems

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Molecular simulation as an aid to experimentalists

(2008) Wilfred F van Gunsteren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

A Role for Confined Water in Chaperonin Function

(2008) Jeremy L. England et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amyloid formation by globular proteins under native conditions

(2008) Fabrizio Chiti et al.   Nature Chemical Biology

Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

(2008) Kathryn A. Scott et al.   STRUCTURE