R. Walker

发表

Benjamin D. Madej, Callum J. Dickson, I. Gould, 2014, Journal of chemical theory and computation.

LIPID11: a modular framework for lipid simulations using amber.

Knut Teigen, Ross C Walker, Benjamin D. Madej, 2012, The journal of physical chemistry. B.

GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Callum J. Dickson, I. Gould, Robin M. Betz, 2012 .

Single Active Site Mutation Causes Serious Resistance of HIV Reverse Transcriptase to Lamivudine: Insight from Multiple Molecular Dynamics Simulations

M. Soliman, R. Walker, S. Bhakat, 2015, Cell Biochemistry and Biophysics.

Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.

A. Onufriev, R. Walker, R. Anandakrishnan, 2015, Biophysical journal.

Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems.

A. W. Götz, F. Paesani, R. Walker, 2012, Journal of chemical theory and computation.

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.

A. Roitberg, S. Le Grand, R. Walker, 2015, Journal of chemical theory and computation.

Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.

Ross C Walker, Adrian E Roitberg, A. Roitberg, 2009, The journal of physical chemistry. A.

Simulating Water Exchange to Buried Binding Sites.

M. Gilson, R. Walker, Tom Kurtzman, 2018, Journal of chemical theory and computation.

Role of the hinge and C-gamma-2/C-gamma-3 interface in immunoglobin G1 Fc domain motions: implications for Fc engineering

J. Prestegard, W. Lanzilotta, R. Walker, 2014 .

Developing improved MD codes for understanding processive cellulases

E. Uberbacher, M. Himmel, C. Brooks, 2008 .

Ligand Binding Pathways and Conformational Transitions of the HIV Protease.

Chia-en A. Chang, J. Mccammon, Yu‐ming M. Huang, 2018, Biochemistry.

Simulation of lipid bilayer self-assembly using all-atom lipid force fields.

Benjamin D. Madej, Callum J. Dickson, I. Gould, 2016, Physical chemistry chemical physics : PCCP.

MAPAS: a tool for predicting membrane-contacting protein surfaces

Igor F Tsigelny, Yuriy Sharikov, Ross C Walker, 2008, Nature Methods.

pH‐dependent conformational dynamics of beta‐secretase 1: A molecular dynamics study

J. Mccammon, R. Walker, D. Mermelstein, 2018, Journal of molecular recognition : JMR.

Computational Approaches to Study Cellulose Hydrolysis

M. Crowley, R. Walker, 2009 .

Complement Factor H and Simian Virus 40 bind the GM1 ganglioside in distinct conformations.

T. Stehle, R. Walker, U. Neu, 2016, Glycobiology.

Influence of N-Myristylation and Ligand Binding on the Flexibility of the Catalytic Subunit of Protein Kinase A

Levi C. T. Pierce, Susan S. Taylor, David A. Johnson, 2013, Biochemistry.

Grain-boundary type and distribution in silicon carbide coatings and wafers

E. López‐Honorato, R. Walker, F. Cancino-Trejo, 2018 .

Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics

D. Mathews, E. Phizicky, R. Walker, 2014, Journal of chemical theory and computation.

An extensible interface for QM/MM molecular dynamics simulations with AMBER

Andreas W. Götz, Matthew A. Clark, Ross C. Walker, 2014, J. Comput. Chem..

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

Duncan Poole, Ross C Walker, Scott Le Grand, 2013, Journal of chemical theory and computation.

SPFP: Speed without compromise - A mixed precision model for GPU accelerated molecular dynamics simulations

Andreas W. Götz, Ross C. Walker, Scott M. Le Grand, 2013, Comput. Phys. Commun..

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Duncan Poole, Dong Xu, Andreas W. Götz, 2012, Journal of chemical theory and computation.

An overview of the Amber biomolecular simulation package

Ross C. Walker, David A. Case, Romelia Salomon-Ferrer, 2013 .

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

Michael K. Gilson, Ross C. Walker, Tom Kurtzman, 2016, J. Comput. Chem..

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

Levi C. T. Pierce, Ross C. Walker, Levi C.T. Pierce, 2012, Journal of chemical theory and computation.

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

Tai-Sung Lee, Darrin M York, Charles Lin, 2018, J. Chem. Inf. Model..

CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations

J Andrew McCammon, Giulia Palermo, Yinglong Miao, 2017, Proceedings of the National Academy of Sciences.

Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations

J. Andrew McCammon, Giulia Palermo, Ross C. Walker, 2016, ACS central science.

Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase

David R. Klug, Ross C. Walker, Ian R. Gould, 2002 .

Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose Iβ

M. Himmel, C. Brooks, J. Brady, 2008 .

Mechanism of 150-cavity formation in influenza neuraminidase

Robert V. Swift, Rommie E. Amaro, Ross C. Walker, 2011, Nature communications.

A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field.

Benjamin D. Madej, I. Gould, R. Walker, 2015, The journal of physical chemistry. B.

mRNA codon optimization with quantum computers

R. Walker, Dillion M. Fox, Kim M Branson, 2021, PloS one.

mRNA codon optimization on quantum computers

R. Walker, K. Branson, Dillion M. Fox, 2021, bioRxiv.

Molecular modeling suggests induced fit of Family I carbohydrate-binding modules with a broken-chain cellulose surface.

M. Himmel, J. Brady, M. Crowley, 2007, Protein engineering, design & selection : PEDS.

Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk)

Levi C. T. Pierce, Sheng Li, Ross C. Walker, 2013, PLoS Comput. Biol..

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.

Ross C Walker, Joseph W Kaus, Levi T Pierce, 2013, Journal of chemical theory and computation.

The implementation of a fast and accurate QM/MM potential method in Amber

Ross C. Walker, Michael F. Crowley, David A. Case, 2008, J. Comput. Chem..

RNA folding using quantum computers

Christopher M. MacDermaid, Christopher M MacDermaid, M. Zwierzyna, 2021, bioRxiv.

Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

Å. A. Skjevik, R. Walker, Louis Noodleman, 2016, Data in brief.

Adaptive mutations alter antibody structure and dynamics during affinity maturation.

I. Wilson, M. Oda, R. Stanfield, 2015, Biochemistry.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

William Sinko, Levi C. T. Pierce, J. Andrew McCammon, 2014, Journal of chemical theory and computation.

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields.

Benjamin D. Madej, Callum J. Dickson, I. Gould, 2015, Chemical communications.

Lipid21: Complex Lipid Membrane Simulations with AMBER

Callum J. Dickson, I. Gould, R. Walker, 2022, Journal of chemical theory and computation.

fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems.

J. Mendieta, James P. Lewis, P. Gómez-Puertas, 2014, Journal of chemical theory and computation.

A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Systems.

Carlos Simmerling, Ross C Walker, Christina Bergonzo, 2009, International journal of quantum chemistry.

Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein.

Christine M Isborn, Todd J Martínez, Ross C Walker, 2012, Journal of chemical theory and computation.

Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.

Å. A. Skjevik, R. Walker, Louis Noodleman, 2016, Biochimica et biophysica acta.

A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

Ilkay Altintas, Rommie E. Amaro, Rommie E Amaro, 2017, Biophysical journal.

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

Andrew Jones, Noam Bernstein, Andreas W. Götz, 2014, J. Comput. Chem..

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

Ross C. Walker, Robin M. Betz, Robin M. Betz, 2015, J. Comput. Chem..

Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

R. Walker, Louis Noodleman, J. Fee, 2014, Inorganic chemistry.

Why Graphics Processing Units

Andreas W. Götz, Ross C. Walker, Perri Needham, 2016 .

Carbinolamine Formation and Dehydration in a DNA Repair Enzyme Active Site

R. Lloyd, R. Walker, M. L. Dodson, 2012, PloS one.

Developing improved MD codes for understanding processive cellulases

E. Uberbacher, M. Himmel, C. Brooks, 2008 .

Assessment of standard force field models against high‐quality ab initio potential curves for prototypes of π–π, CH/π, and SH/π interactions

Bobby G. Sumpter, Ross C. Walker, Ian R. Gould, 2009, J. Comput. Chem..

Electronic Structure Calculations on Graphics Processing Units From Quantum Chemistry to Condensed Matter Physics

Ross C. Walker, R. Walker, Andreas W. Goetz, 2016 .

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Ross C. Walker, Charles Lin, Daniel J. Mermelstein, 2018, bioRxiv.

Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package.

Ross C Walker, Adrian E Roitberg, Marcus Elstner, 2007, The journal of physical chemistry. A.

Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex.

Ross C Walker, Michael E Himmel, Michael F Crowley, 2009, Carbohydrate research.

CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software

Ross C. Walker, Michael F. Crowley, Mark J. Williamson, 2009 .

Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase

Robert V. Swift, Rommie E Amaro, Lane Votapka, 2012, Journal of molecular and genetic medicine : an international journal of biomedical research.

Quantum Chemistry on Graphics Processing Units

Andreas W. Götz, Ross C. Walker, Thorsten Wölfle, 2010 .

Single Active Site Mutation Causes Serious Resistance of HIV Reverse Transcriptase to Lamivudine: Insight from Multiple Molecular Dynamics Simulations

M. Soliman, R. Walker, S. Bhakat, 2016, Cell Biochemistry and Biophysics.

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

F. Jensen, R. Walker, Julie Grouleff, 2015, The journal of physical chemistry. B.

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy

Rommie E. Amaro, J Andrew McCammon, Morgan Lawrenz, 2010, Proteins.

Developing improved MD and QMMM codes for modeling enzymes essential to biomass liquid fuel production

C. Brooks, E. Knoll, M. Crowley, 2011 .

A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus.

R. Walker, Louis Noodleman, Longhua Yang, 2016, Physical chemistry chemical physics : PCCP.

X-ray crystallographic and molecular dynamic analyses of Drosophila melanogaster embryonic muscle myosin define domains responsible for isoform-specific properties.

T. Huxford, S. Bernstein, R. Walker, 2019, Journal of molecular biology.

Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations

David R. Klug, Ross C. Walker, Ian R. Gould, 2007, J. Comput. Chem..

An investigation of the effects of error correcting code on GPU-accelerated molecular dynamics simulations

Ross C. Walker, Robin M. Betz, Robin M. Betz, 2013, XSEDE.

Extension of the AMBER molecular dynamics software to Intel's Many Integrated Core (MIC) architecture

Ross C. Walker, Ashraf Bhuiyan, Perri J. Needham, 2016, Comput. Phys. Commun..

Immunoglobulin G1 Fc domain motions: implications for Fc engineering.

J. Prestegard, W. Lanzilotta, R. Walker, 2014, Journal of molecular biology.

Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution

Andreas W. Götz, Ross C. Walker, Marat Valiev, 2017, J. Comput. Chem..

Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units

Dong Xu, Ross C. Walker, Mark J. Williamson, 2010 .

Adaptive mutations alter antibody structure and dynamics during affinity maturation.

I. Wilson, M. Oda, R. Stanfield, 2015, Biochemistry.

An extensible interface for QM/MM molecular dynamics simulations with AMBER

R. Walker, M. Clark, A. Götz, 2014, J. Comput. Chem..

Ligand Binding Pathways and Conformational Transitions of the HIV Protease.

Yu‐ming M. Huang, R. Walker, Chia‐en A. Chang, 2018, Biochemistry.

Simulating Water Exchange to Buried Binding Sites.

M. Gilson, R. Walker, I. Ben-Shalom, 2018, Journal of chemical theory and computation.

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation

Levi C. T. Pierce, W. Sinko, Denis Bucher, 2014, Journal of chemical theory and computation.

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

S. Le Grand, R. Walker, D. Poole, 2013, Journal of chemical theory and computation.

Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study

A. Roitberg, R. Walker, G. Seabra, 2008 .

A practical introduction to molecular dynamics simulations: applications to homology modeling.

Alessandra Nurisso, Antoine Daina, Ross C Walker, 2012, Methods in molecular biology.

Advances in Rosetta protein structure prediction on massively parallel systems

Srivatsan Raman, R. Walker, Bin Qian, 2008, IBM J. Res. Dev..