Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

(2018) Matthew P. Kroonblawd et al.   Journal of Chemical Theory and Computation

Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics

(2017) Rui Sun et al.   Journal of Chemical Theory and Computation

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks

(2016) Lin Shen et al.   Journal of Chemical Theory and Computation

ATP Hydrolysis Mechanism in a Maltose Transporter Explored by QM/MM Metadynamics Simulation

(2016) Wei-Lin Hsu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

Catalytic Mechanism of the Maltose Transporter Hydrolyzing ATP

(2015) Wenting Huang et al.   BIOCHEMISTRY

Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations

(2015) Pedro Ojeda-May et al.   JOURNAL OF CHEMICAL PHYSICS

Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase

(2015) Pedro Ojeda-May et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalytic Mechanism of Bacteriophage T4 Rad50 ATP Hydrolysis

(2014) Timothy J. Herdendorf et al.   BIOCHEMISTRY

Generating Symmetry in the Asymmetric ATP-binding Cassette (ABC) Transporter Pdr5 fromSaccharomyces cerevisiae

(2014) Rakeshkumar P. Gupta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations

(2014) Yan Zhou et al.   Journal of Chemical Theory and Computation

Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches

(2014) Kwangho Nam   Journal of Chemical Theory and Computation

How Accurate Are Transition States from Simulations of Enzymatic Reactions?

(2014) Dvir Doron et al.   Journal of Chemical Theory and Computation

Enzymatic Minimum Free Energy Path Calculations Using Swarms of Trajectories

(2014) Melchor Sanchez-Martinez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unraveling the Mystery of ATP Hydrolysis in Actin Filaments

(2014) Martin McCullagh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Catalytic strategy used by the myosin motor to hydrolyze ATP

(2014) F. A. Kiani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter

(2014) M. Hohl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrolysis at One of the Two Nucleotide-binding Sites Drives the Dissociation of ATP-binding Cassette Nucleotide-binding Domain Dimers

(2013) Maria E. Zoghbi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies

(2013) Kirill Zinovjev et al.   Journal of Chemical Theory and Computation

Isotropic Periodic Sum Treatment of Long-Range Electrostatic Interactions in Combined Quantum Mechanical and Molecular Mechanical Calculations

(2013) Pedro Ojeda-May et al.   Journal of Chemical Theory and Computation

H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB

(2013) Yan Zhou et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation

(2012) Michael Hohl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Characterization of the E506Q and H537A Dysfunctional Mutants in theE. coliABC Transporter MsbA

(2011) Kathryn M. Schultz et al.   BIOCHEMISTRY

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

(2011) Victor Ovchinnikov et al.   JOURNAL OF CHEMICAL PHYSICS

Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations

(2011) Edina Rosta et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pore opening and closing of a pentameric ligand-gated ion channel

(2010) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Substrate-assisted catalysis: Molecular basis and biological significance

(2010) William Dall'Acqua et al.   PROTEIN SCIENCE

The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter

(2009) Erik Procko et al.   FASEB JOURNAL

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

(2009) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

On-the-path random walk sampling for efficient optimization of minimum free-energy path

(2009) Mengen Chen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Finding Transition Pathways Using the String Method with Swarms of Trajectories

(2008) Albert C. Pan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Quantum Mechanical/Molecular Mechanical Simulation Study of the Mechanism of Hairpin Ribozyme Catalysis

(2008) Kwangho Nam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

(2008) A. L. Davidson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

(2008) L. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5

(2008) Robert Ernst et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA