New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations

(2017) Mark S. Miller et al.   Journal of Chemical Theory and Computation

Direct Comparison of Amino Acid and Salt Interactions with Double-Stranded and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

(2017) Casey T. Andrews et al.   Journal of Chemical Theory and Computation

Reparameterization of Solute—Solute Interactions for Amino Acid–Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations

(2017) Wesley K. Lay et al.   Journal of Chemical Theory and Computation

Large-Conductance Transmembrane Porin Made from DNA Origami

(2016) Kerstin Göpfrich et al.   ACS Nano

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields

(2016) Jejoong Yoo et al.   BIOPOLYMERS

Water-Mediated Ion Pairing: Occurrence and Relevance

(2016) Nico F. A. van der Vegt et al.   CHEMICAL REVIEWS

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

(2016) Petra Kührová et al.   Journal of Chemical Theory and Computation

Optimizing Solute–Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements

(2016) Wesley K. Lay et al.   Journal of Chemical Theory and Computation

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

(2016) Alexey K. Shaytan et al.   JOURNAL OF MOLECULAR BIOLOGY

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

(2016) Mark S. Miller et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations

(2016) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Ion Channels Made from a Single Membrane-Spanning DNA Duplex

(2016) Kerstin Göpfrich et al.   NANO LETTERS

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Molecular mechanics of DNA bricks:in situstructure, mechanical properties and ionic conductivity

(2016) Scott Michael Slone et al.   NEW JOURNAL OF PHYSICS

The structure and intermolecular forces of DNA condensates

(2016) Jejoong Yoo et al.   NUCLEIC ACIDS RESEARCH

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

(2016) Jejoong Yoo et al.   Nature Communications

Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field

(2015) Chen-Yu Li et al.   ACS Nano

Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations

(2015) Vishal Maingi et al.   ACS Nano

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment

(2015) Reid F. Brown et al.   Journal of Chemical Theory and Computation

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

(2015) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

(2015) Jejoong Yoo et al.   Journal of Chemical Theory and Computation

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

(2015) Carsten Kutzner et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating

(2015) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Neurotransmitter and psychostimulant recognition by the dopamine transporter

(2015) Kevin H. Wang et al.   NATURE

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Physicochemical Properties of Cells and Their Effects on Intrinsically Disordered Proteins (IDPs)

(2014) Francois-Xavier Theillet et al.   CHEMICAL REVIEWS

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

(2014) Konstantinos Gkionis et al.   Journal of Chemical Theory and Computation

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules

(2014) Jeffrey Comer et al.   Journal of Chemical Theory and Computation

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

(2014) Robert B. Best et al.   Journal of Chemical Theory and Computation

Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms

(2014) Emilia L. Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Benchmarking all-atom simulations using hydrogen exchange

(2014) John J. Skinner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Drazen Petrov et al.   PLoS Computational Biology

A Comparison of DNA Compaction by Arginine and Lysine Peptides: A Physical Basis for Arginine Rich Protamines

(2013) Jason DeRouchey et al.   BIOCHEMISTRY

Ion Competition in Condensed DNA Arrays in the Attractive Regime

(2013) Xiangyun Qiu et al.   BIOPHYSICAL JOURNAL

Optimizing Protein–Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field

(2013) Dail E. Chapman et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Quantum and All-Atom Molecular Dynamics Simulations of Protonation and Divalent Ion Binding to Phosphatidylinositol 4,5-Bisphosphate (PIP2)

(2013) David R. Slochower et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data

(2013) Richard M. Venable et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

(2013) J. Yoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

(2012) Lacramioara Bintu et al.   CELL

Hofmeister Phenomena: An Update on Ion Specificity in Biology

(2012) Pierandrea Lo Nostro et al.   CHEMICAL REVIEWS

Computational studies of molecular machines: the ribosome

(2012) Karissa Y Sanbonmatsu   CURRENT OPINION IN STRUCTURAL BIOLOGY

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

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

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

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

Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations

(2012) Jejoong Yoo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Slowing down DNA Translocation through a Nanopore in Lithium Chloride

(2012) Stefan W. Kowalczyk et al.   NANO LETTERS

End-to-end attraction of duplex DNA

(2012) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Systematic Validation of Protein Force Fields against Experimental Data

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

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

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

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Protein Dynamics: Moore's Law in Molecular Biology

(2011) Michele Vendruscolo et al.   CURRENT BIOLOGY

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ion Pairing in Aqueous Electrolyte Solutions with Biologically Relevant Anions

(2011) Pritam Ganguly et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Membrane protein sequestering by ionic protein–lipid interactions

(2011) Geert van den Bogaart et al.   NATURE

Salt-Dependent DNA-DNA Spacings in Intact BacteriophageλReflect Relative Importance of DNA Self-Repulsion and Bending Energies

(2011) Xiangyun Qiu et al.   PHYSICAL REVIEW LETTERS

How Fast-Folding Proteins Fold

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

Role of Histone Tails in Structural Stability of the Nucleosome

(2011) Mithun Biswas et al.   PLoS Computational Biology

Chemical versus Mechanical Perturbations on the Protonation State of Arginine in Complex Lipid Membranes: Insights from Microscopic pKa Calculations

(2010) Jejoong Yoo et al.   BIOPHYSICAL JOURNAL

Measuring and Modeling Activity Coefficients in Aqueous Amino-Acid Solutions

(2010) Christoph Held et al.   INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH

Computational Design and Experimental Testing of the Fastest-Folding β-Sheet Protein

(2010) Stefano Piana et al.   JOURNAL OF MOLECULAR BIOLOGY

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor

(2010) Michael P. Bokoch et al.   NATURE

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Running in Reverse: The Structural Basis for Translocation Polarity in Hexameric Helicases

(2009) Nathan D. Thomsen et al.   CELL

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions

(2009) Christopher J. Fennell et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

(2009) Yun Luo et al.   Journal of Physical Chemistry Letters

Cation specific binding with protein surface charges

(2009) B. Hess et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PIP2 Is a Necessary Cofactor for Ion Channel Function: How and Why?

(2008) Byung-Chang Suh et al.   Annual Review of Biophysics

Physical Chemistry of DNA Viruses

(2008) Charles M. Knobler et al.   Annual Review of Physical Chemistry

Attractive Forces between Cation Condensed DNA Double Helices

(2008) Brian A. Todd et al.   BIOPHYSICAL JOURNAL

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

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

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydration Water Dynamics Near Biological Interfaces†

(2008) Margaret E. Johnson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Attraction in Monovalent and Divalent Electrolytes

(2008) Binquan Luan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Membrane recognition by phospholipid-binding domains

(2008) Mark A. Lemmon   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

(2008) Liang Dai et al.   PHYSICAL REVIEW LETTERS

The vapour pressures over saturated aqueous solutions of dl-2-aminobutyric acid, 4-aminobutyric acid, sodium-d-gluconate, sodium hippurate, and potassium magnesium-l-aspartate

(2007) Alexander Apelblat et al.   JOURNAL OF CHEMICAL THERMODYNAMICS