J. Brady

发表

Translational and rotational dynamics of monosaccharide solutions.

Gerald Lelong, W. Howells, J. Brady, 2009, The journal of physical chemistry. B.

Biomass Recalcitrance: Engineering Plants and Enzymes for Biofuels Production

David K. Johnson, T. Foust, M. Himmel, 2007, Science.

The interaction of guanidinium ions with a model peptide.

J. Brady, C. Dempsey, John W Brady, 2007, Biophysical journal.

The polysaccharide extracted from the biofilm of Burkholderia multivorans strain C1576 binds hydrophobic species and exhibits a compact 3D-structure.

J. Brady, S. Bosi, R. Rizzo, 2019, International journal of biological macromolecules.

Computer simulation studies of microcrystalline cellulose Iβ

M. Himmel, J. Brady, J. Sugiyama, 2006 .

Simulation studies of substrate recognition by the exocellulase CelF from Clostridium cellulolyticum

M. Himmel, J. Brady, D. Wilson, 2016, Biotechnology and bioengineering.

Experimental and modeling studies of an unusual water-filled pore structure with possible mechanistic implications in family 48 cellulases.

M. Himmel, J. Brady, Y. Bomble, 2014, The journal of physical chemistry. B.

The effect of hydration upon the conformation and dynamics of neocarrabiose, a repeat unit of β‐carrageenan

J. Brady, K. Ueda, 1996, Biopolymers.

Conformational Analysis of Oligosaccharides: Reconciliation of Theory with Experiment

A. Imberty, J. Brady, S. Michnick, 1990 .

Nanometer-scale ion aggregates in aqueous electrolyte solutions: guanidinium carbonate.

J. Brady, C. Dempsey, G. W. Neilson, 2006, The journal of physical chemistry. B.

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields.

M. Himmel, J. Brady, M. Crowley, 2012, Journal of chemical theory and computation.

The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered protein.

M. Himmel, J. Brady, Y. Bomble, 2010, Biophysical journal.

Conformational modeling of substrate binding to endocellulase E2 from Thermomonospora fusca.

J. Brady, D. Wilson, J. S. Taylor, 1995, Protein engineering.

The Anomeric Equilibrium in d-Xylose: Free Energy and the Role of Solvent Structuring

M. Karplus, J. Brady, R. Schmidt, 1996 .

Reversible dehydration of trehalose and anhydrobiosis: from solution state to an exotic crystal?

J. Brady, A. Cesàro, C. Skopec, 2001 .

Molecular dynamics simulations of .alpha.-D-glucose in aqueous solution

John W. Brady, J. Brady, 1989 .

Water structuring around complex solutes: theoretical modeling of α-d-glucopyranose

J. Brady, B. Leroux, H. Bizot, 1997 .

Disaccharide conformational flexibility. I. An adiabatic potential energy map for sucrose

J. Brady, V. H. Tran, 1990, Biopolymers.

Overview of computer modeling of cellulose.

J. Brady, Malin Bergenstråhle-Wohlert, 2012, Methods in molecular biology.

Structures of Plant Cell Wall Celluloses

M. Himmel, J. Brady, S. Ding, 2009 .

Molecular dynamics and neutron scattering study of glucose solutions confined in MCM-41.

Gerald Lelong, J. Brady, M. Saboungi, 2011, The journal of physical chemistry. B.

Strategies to reduce end‐product inhibition in family 48 glycoside hydrolases

M. Himmel, J. Brady, Y. Bomble, 2016, Proteins.

Free energy landscapes of the α-d- and β-d-glucopyranose conformations in both vacuum and aqueous solution

J. Brady, M. Saboungi, Gérald Lelong, 2012 .

The application of simulated annealing to the conformational analysis of disaccharides

J. Brady, K. Naidoo, 1997 .

Stacking and Branching in Self-Aggregation of Caffeine in Aqueous Solution: From the Supramolecular to Atomic Scale Clustering.

J. Brady, Y. Gerelli, A. Cesàro, 2016, The journal of physical chemistry. B.

Thermostable variants of bovine β-lactoglobulin

C. Batt, J. Brady, Yunje Cho, 1994 .

Stacking of purines in water: the role of dipolar interactions in caffeine.

J. Brady, S. Di Fonzo, C. Masciovecchio, 2016, Physical chemistry chemical physics : PCCP.

Identification of essential arginyl residues in cytoplasmic malate dehydrogenase with butanedione.

J. Brady, J. H. Harrison, D. Bleile, 1975, The Journal of biological chemistry.

Dynamics of trehalose molecules in confined solutions.

Gerald Lelong, J. Brady, D. Price, 2007, The Journal of chemical physics.

Comparison of the simulations of cellulosic crystals with three carbohydrate force fields.

J. Brady, M. Crowley, H. Miyamoto, 2016, Carbohydrate research.

Computer Modeling of Carbohydrates: An Introduction

J. Brady, A. French, 1990 .

Molecular Dynamics Simulations of α-D-Glucose.

J. Brady, 1987 .

Reversible dehydration of trehalose and anhydrobiosis: from solution state to an exotic crystal?

J. Brady, A. Cesàro, C. Skopec, 2001, Carbohydrate research.

Weakly hydrated surfaces and the binding interactions of small biological solutes

M. Himmel, J. Brady, M. Saboungi, 2012, European Biophysics Journal.

Hydrolysis of Cellulose and Hemicellulose

Stephen R. Decker, Liisa Viikari, Michael E. Himmel, 2004 .

Free energy surfaces for the interaction of D-glucose with planar aromatic groups in aqueous solution.

J. Brady, J. Wohlert, U. Schnupf, 2010, The Journal of chemical physics.

Preferential interactions of guanidinum ions with aromatic groups over aliphatic groups.

J. Brady, C. Dempsey, P. Mason, 2009, Journal of the American Chemical Society.

The structure of aqueous guanidinium chloride solutions.

Alexander D. MacKerell, Alexander D MacKerell, J. Brady, 2004, Journal of the American Chemical Society.

Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.

J. Brady, M. Saboungi, P. Mason, 2011, The journal of physical chemistry. B.

Computer Modeling Studies of the Interaction of Water With Carbohydrates

J. Brady, K. Tasaki, R. Schmidt, 1994 .

Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis

Bruce Tidor, Jiali Gao, Martin Karplus, 1991 .

Anisotropic Solvent Structuring in Aqueous Sugar Solutions

J. Brady, Qiang Liu and, 1996 .

The role of hydrogen bonding in carbohydrates: molecular dynamics simulations of maltose in aqueous solution

J. Brady, R. Schmidt, 1993 .

Water mobility in the dehydration of crystalline trehalose

J. Brady, A. Cesàro, C. Skopec, 2010 .

Burkholderia cenocepacia h111 produces a water-insoluble exopolysaccharide in biofilm Structural determination and molecular modelling

J. Brady, T. Tolker-Nielsen, N. Ravenscroft, 2020 .

Ramachandran Conformational Energy Maps for Disaccharide Linkages found in Burkholderia multivorans Biofilm Polysaccharides.

J. Brady, M. Caterino, Ining A. Jou, 2019, International journal of biological macromolecules.

Additive empirical force field for hexopyranose monosaccharides

Alexander D. MacKerell, Ganesh Kamath, Olgun Guvench, 2008, J. Comput. Chem..

Inter‐residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations

J. Brady, G. Widmalm, O. Engström, 2019, Chembiochem : a European journal of chemical biology.

Caffeine and sugars interact in aqueous solutions: a simulation and NMR study.

M. Himmel, J. Brady, M. Saboungi, 2012, The journal of physical chemistry. B.

Design improvements of β-lactoglobulin

Carl A. Batt, John W. Brady, Lindsay Sawyer, 1994 .

Simulation studies of the insolubility of cellulose.

M. Himmel, J. Brady, J. Wohlert, 2010, Carbohydrate research.

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

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

Molecular Dynamics Studies of the Hydration of α,α-Trehalose

P. Karplus, J. Brady, Qiang Liu, 1997 .

Disaccharide conformational flexibility. II. Molecular dynamics simulations of sucrose

J. Brady, V H Tran, J W Brady, 1990, Biopolymers.

Calculation of the Potential of Mean Force for the Binding of Glucose to Benzene in Aqueous Solution

John W. Brady, J. Brady, R. Palma, 2000 .

Velocity dependence of angular distributions in gas/solid--surface collisions: Relationship to the interaction potential

J. Doll, J. Brady, D. Thompson, 1978 .

Concentration enrichment of urea at cellulose surfaces: results from molecular dynamics simulations and NMR spectroscopy

J. Brady, L. Berglund, J. Wohlert, 2012, Cellulose.

Specificity of ion-protein interactions: complementary and competitive effects of tetrapropylammonium, guanidinium, sulfate, and chloride ions.

Pavel Jungwirth, J. Heyda, J. Brady, 2009, The journal of physical chemistry. B.

Structure of aqueous glucose solutions as determined by neutron diffraction with isotopic substitution experiments and molecular dynamics calculations.

J. Brady, M. Saboungi, J. Enderby, 2005, The journal of physical chemistry. B.

The conformation of a ribose derivative in aqueous solution: a neutron-scattering and molecular dynamics study.

J. Brady, M. Saboungi, C. Bush, 2013, Biopolymers.

Molecular dynamics simulations of β-d-glucopyranose

J. Brady, 1987 .

Physico-chemical properties of aqueous drug solutions: From the basic thermodynamics to the advanced experimental and simulation results.

J. Brady, A. Gamini, B. Bellich, 2018, International journal of pharmaceutics.

Water structuring over the hydrophobic surface of cellulose.

J. Brady, H. Miyamoto, U. Schnupf, 2014, Journal of agricultural and food chemistry.

Simulation and Neutron Diffraction Studies of Small Biomolecules in Water

J. Brady, D. Price, M. Saboungi, 2011, Food biophysics.

Molecular dynamics studies of the conformation of sorbitol.

J. Brady, M. Saboungi, R. Pastor, 2009, Carbohydrate research.

Neutron diffraction and simulation studies of the exocyclic hydroxymethyl conformation of glucose.

J. Brady, M. Saboungi, G. Cuello, 2006, The Journal of chemical physics.

MODEL DEPENDENCE OF THE ANISOTROPIC STRUCTURING OF SOLVENT WATER AROUND SUGARS IN MOLECULAR DYNAMICS SIMULATIONS

J. Brady, Qiang Liu, 1997 .

Intramolecular vibrational relaxation of CH stretch overtones in benzene

J. Brady, D. Thompson, Karen L. Bintz, 1987 .

Classical dynamics study of intramolecular energy flow in benzene

J. Brady, D. Thompson, Karen L. Bintz, 1986 .

Influence of anharmonicity of “bath” modes on intramolecular energy transfer from a local mode

J. Brady, D. Thompson, Karen L. Bintz, 1986 .

Cluster dynamics: A classical trajectory study of A*n→An−1+A

J. D. Doll, J. Doll, J. Brady, 1979 .

Model Dependence of the Anisotropic Structuring of Solvent Water Around Sugars in Molecular Dynamics (MD) Simulations

J. Brady, Qi Yong Liu, 1997 .

Ligand binding to G-quadruplex DNA: new insights from ultraviolet resonance Raman spectroscopy.

J. Brady, B. Pagano, F. D'Aria, 2020, Physical chemistry chemical physics : PCCP.

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.

Molecular dynamics simulations of a winter flounder “antifreeze” polypeptide in aqueous solution

J. Brady, P. Clancy, S. McDonald, 1993, Biopolymers.

Cel48A from Thermobifida fusca: Structure and site directed mutagenesis of key residues

M. Himmel, J. Brady, D. Wilson, 2014, Biotechnology and bioengineering.

Natural diversity of glycoside hydrolase family 48 exoglucanases: insights from structure

M. Himmel, D. Sammond, J. Brady, 2017, Biotechnology for Biofuels.

Natural diversit y of gly coside hydrolase family 48 exoglucanases : insights fr om struc ture

M. Himmel, D. Sammond, J. Brady, 2017 .

Computer modeling of carbohydrate molecules

Alfred D. French, John W. Brady, J. Brady, 1990 .

Glucose interactions with a model peptide

J. Brady, M. Saboungi, C. Dempsey, 2011, Proteins.

Potential of mean force conformational energy maps for disaccharide linkages of the Burkholderia multivorans exopolysaccharide C1576 in aqueous solution.

J. Brady, A. Yoo, Ining A. Jou, 2023, Carbohydrate research.

Theoretical studies of oligosaccharide structure and conformational dynamics

J. Brady, 1991 .

Molecular Dynamics Simulations of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Chloride and Its Binary Mixtures with Ethanol.

J. Brady, J. Wohlert, G. Widmalm, 2014, Journal of chemical theory and computation.

"Tetrahedrality" and the relationship between collective structure and radial distribution functions in liquid water.

J. Brady, P. E. Mason, 2007, Journal of Physical Chemistry B.

Water structuring above solutes with planar hydrophobic surfaces.

J. Brady, U. Schnupf, 2017, Physical chemistry chemical physics : PCCP.

A classical trajectory study of xenon atom–chlorine dimer collisions

J. D. Doll, J. Doll, J. Brady, 1980 .

Water Confined in Cylindrical Pores: A Molecular Dynamics Study

Gerald Lelong, J. Brady, M. Saboungi, 2011, Food biophysics.

Molecular dynamics simulations of the whey protein ß-lactoglobulin

J. Brady, W. Gu, 1992 .

The biofilm of Burkholderia cenocepacia H111 contains an exopolysaccharide composed of l-rhamnose and l-mannose: Structural characterization and molecular modelling.

J. Brady, T. Tolker-Nielsen, N. Ravenscroft, 2020, Carbohydrate research.

Hydration of Caffeine at High Temperature by Neutron Scattering and Simulation Studies.

J. Brady, M. Saboungi, F. Bruni, 2015, The journal of physical chemistry. B.

A revised potential-energy surface for molecular mechanics studies of carbohydrates.

J. Brady, S. Ha, A Giammona, 1988, Carbohydrate research.

A new structural technique for examining ion-neutral association in aqueous solution.

J. Brady, D. Price, M. Saboungi, 2013, Faraday discussions.

Classical Trajectory Studies of the Formation and Unimolecular Decay of Rare Gas Clusters

J. D. Doll, J. Doll, J. Brady, 1981 .

Conformational Flexibility of Sucrose: Static and Dynamical Modeling

J. Brady, V. H. Tran, 1990 .

Conformational analysis and molecular dynamics simulations of maltose

J. Brady, S. Ha, L. J. Madsen, 1988, Biopolymers.

Molecular Dynamics Simulations of Carbohydrates and Their Solvation

J. Brady, S. Ha, V. H. Tran, 1990 .

FREE ENERGY SIMULATION STUDIES OF THE BINDING SPECIFICITY OF MANNOSE-BINDING PROTEIN

John W. Brady, J. Brady, R. K. Schmidt, 1996 .

Molecular dynamics simulations of .alpha.-D-glucose

John W. Brady, J. Brady, 1986 .

Molecular dynamics simulations of a glycoprotein: the lectin from Erythrina corallodendron

J. Brady, K. Naidoo, 1997 .

Simulations of the aqueous solvation of trilaurin

J. Brady, J. Sherbon, S. Engelsen, 1994 .

Molecular Dynamics and Neutron Scattering Studies of Potassium Chloride in Aqueous Solution.

J. Brady, M. Saboungi, T. Ichiye, 2019, The journal of physical chemistry. B.

Sugar-binding sites on the surface of the carbohydrate-binding module of CBH I from Trichoderma reesei.

Udo Schnupf, Michael E Himmel, Attilio Cesàro, 2011, Carbohydrate research.

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.

Cluster dynamics: Further classical trajectory studies of A+An⇄A*n+1

J. Doll, J. Brady, D. Thompson, 1980 .

Crowding and conformation interplay on human DNA G-quadruplex by ultraviolet resonant Raman scattering.

Silvia Di Fonzo, Luigi Petraccone, Cettina Bottari, 2019, Physical chemistry chemical physics : PCCP.

Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations

Kevin J. Naidoo, Michelle Kuttel, J. W. Brady, 2002, J. Comput. Chem..

The reversal by sulfate of the denaturant activity of guanidinium.

J. Brady, C. Dempsey, P. Mason, 2007, Journal of the American Chemical Society.

MOLECULAR DYNAMICS SIMULATIONS OF CARRABIOSE

J. Brady, K. Ueda, 1997 .

Molecular dynamics of glucose in solution: a quasielastic neutron scattering study.

J. Brady, D. Price, M. Saboungi, 2004, The Journal of chemical physics.

Aromatic residues surrounding the active site tunnel of TfCel48A influence activity, processivity, and synergistic interactions with other cellulases

J. Brady, K. Hefferon, D. Wilson, 2019, Biotechnology and Bioengineering.

Observations concerning the treatment of long‐range interactions in molecular dynamics simulations

K. Tasaki, S. McDonald, J. W. Brady, 1993, J. Comput. Chem..

Molecular dynamics of confined glucose solutions.

Gerald Lelong, J. Brady, D. Price, 2005, The Journal of chemical physics.

Conformational dynamics and acoustic absorption in protein solution

J. Brady, L. Slutsky, C. Allin, 1989, Proceedings., IEEE Ultrasonics Symposium,.

Energetics for displacing a single chain from the surface of microcrystalline cellulose into the active site of Acidothermus cellulolyticus Cel5A.

M. Himmel, J. Brady, J. Matthews, 2003, Protein Engineering.

Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

J. Brady, R. Oswald, K. A. McGroddy, 1994, Biophysical journal.

Molecular dynamics simulation of the aqueous solvation of sugars.

J. Brady, S. Ha, 1991, Advances in experimental medicine and biology.

The Interaction of Sorbitol with Caffeine in Aqueous Solution

J. Brady, A. Cesàro, L. Tavagnacco, 2013, Food Biophysics.

Molecular Mechanics Studies of Cellulases

Michael E. Himmel, Pierfrancesco Zuccato, John W. Brady, 2000 .

Burkholderiacenocepacia H111 Produces a Water-Insoluble Exopolysaccharide in Biofilm: Structural Determination and Molecular Modelling

J. Brady, T. Tolker-Nielsen, N. Ravenscroft, 2020, International journal of molecular sciences.

Role of Glucose in Enhancing Stability of Aqueous Silica Gels Against Dehydration

J. Brady, D. Price, M. Saboungi, 2012 .

Neutron diffraction studies on aqueous solutions of glucose

John E. Enderby, John W. Brady, J. Brady, 2003 .

Calculation of the Ramachandran Potential of Mean Force for a Disaccharide in Aqueous Solution

Kevin J. Naidoo, John W. Brady, J. Brady, 1999 .

AND UNIMOLECULAR DECAY OF RARE GAS CLUSTERS

J. D. Doll, J. Doll, J. Brady, 1981 .

The conformational free-energy map for solvated neocarrabiose.

J. Brady, K. Ueda, H. Nakayama, 2004, Carbohydrate research.

Myelography iodinated contrast media. I. Unraveling the atropisomerism properties in solution.

J. Brady, A. Maiocchi, L. Fontanive, 2015, Molecular pharmaceutics.