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List of works by Jeremy C Smith

"To Be or Not to Be" Protonated: Atomic Details of Human Carbonic Anhydrase-Clinical Drug Complexes by Neutron Crystallography and Simulation.

scientific article published on 29 January 2018

A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop.

scientific article

A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction

scientific article published on 31 July 2019

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils

scientific article published on 13 July 2011

A Structural Study of CESA1 Catalytic Domain of Arabidopsis Cellulose Synthesis Complex: Evidence for CESA Trimers

scientific article published on 10 November 2015

A closed-loop model of the respiratory system: focus on hypercapnia and active expiration

scientific article

A common pharmacophoric footprint for AIDS vaccine design

scientific article published in July 2004

A computationally identified compound antagonizes excess FGF-23 signaling in renal tubules and a mouse model of hypophosphatemia

scientific article published on 22 November 2016

A molecular mechanics force field for biologically important sterols

scientific article published in October 2005

A molecular mechanics force field for lignin.

scientific article

AM1/d Parameters for Magnesium in Metalloenzymes

scientific article published on 01 July 2006

Ab initio study of molecular interactions in cellulose Iα.

scientific article published on 28 August 2013

Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer

scientific article published on April 2014

Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions

scientific article published on October 2010

Alteration of water structure by peptide clusters revealed by neutron scattering in the small-angle region (below 1 Å(-1))

scientific article

Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping

scientific article published on 01 July 2006

Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21.

scientific article

Biological Membrane Organization and Cellular Signaling

scientific article published on 12 February 2019

Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation

scientific article

Can proteins and crystals self-catalyze methyl rotations?

scientific article published on 01 November 2005

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

scientific article published on 01 September 2002

Capturing Deuteration Effects in a Molecular Mechanics Force Field: Deuterated THF and the THF-Water Miscibility Gap

scientific article published on 26 March 2020

Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS ⬇️

scientific article published on October 12, 2010

Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis

scientific article published in September 2009

Charge-based interactions between peptides observed as the dominant force for association in aqueous solution

scientific article

Chemical factors that control lignin polymerization

scientific article published on 30 December 2013

Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations

scientific article published on 6 December 2012

Coarse-grain model for natural cellulose fibrils in explicit water

scientific article published on 05 March 2014

Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.

scientific article

Coarse-grained force field for the nucleosome from self-consistent multiscaling

Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations

scientific article published on 01 December 2009

Community detection in sequence similarity networks based on attribute clustering

scientific article published on 24 July 2017

Computer simulations of the flexibility of a series of synthetic cyclic peptide analogues

scientific article published on 01 August 1993

Configurational distribution of denatured phosphoglycerate kinase

scientific article published on 01 June 1993

Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly

scientific article published on 26 September 2019

Conformational heterogeneity and low-frequency vibrational modes of proteins

scientific article published on 8 November 2006

Convergence in peptide folding simulation: Multiple trajectories of a potential AIDS pharmacophore ⬇️

scientific article published on October 1, 2003

Correlated intramolecular motions and diffuse X-ray scattering in lysozyme

scientific article published on 01 February 1994

Cryosolvents useful for protein and enzyme studies below -100 degrees C.

scientific article

Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering

article

Detection of individual p53-autoantibodies by using quenched peptide-based molecular probes.

scientific article published in December 2002

Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins

scientific article published on 24 March 2018

Determination of cellulose crystallinity from powder diffraction diagrams

scientific article published on 01 February 2015

Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering

scientific article published on 14 October 2016

Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulation Study

article

Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

scientific article published on 6 September 2008

Dynamic Neutron Scattering by Biological Systems.

scientific article published on 21 March 2018

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

scientific article published in November 2013

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.

scientific article

Dynamic simulation of the mouse prion protein

scientific article published on 01 November 2000

Dynamical Transition of Collective Motions in Dry Proteins

scientific article published on 25 July 2017

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

scientific article

Dynamics at a Peptide-TiO2 Anatase (101) Interface

scientific article published on 29 August 2017

Dynamics of immobilized and native Escherichia coli dihydrofolate reductase by quasielastic neutron scattering

scientific article

Dynamics of myoglobin: comparison of simulation results with neutron scattering spectra

scientific article published on February 1990

Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP.

scientific article

Dynamics of water bound to crystalline cellulose

scientific article published on 19 September 2017

Effects of carotenoids on lipid bilayers

scientific article published on 19 January 2018

Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.

scientific article

Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases

scientific article published in November 2009

Engineering of protein epitopes: a single deletion in a snake toxin generates full binding capacity to a previously unrecognized antibody

scientific article published on 01 July 1994

Ensemble Docking in Drug Discovery

scientific article published on 30 March 2018

Ensemble Docking in Drug Discovery: How Many Protein Configurations from Molecular Dynamics Simulations are Needed To Reproduce Known Ligand Binding?

scientific article published on 12 February 2019

Ensemble docking to difficult targets in early-stage drug discovery: Methodology and application to fibroblast growth factor 23.

scientific article published on 25 September 2017

Environmental Mercury Chemistry - In Silico

scientific article published on 28 January 2019

Enzyme activity and dynamics: xylanase activity in the absence of fast anharmonic dynamics

scientific article published in March 2000

Enzyme activity and flexibility at very low hydration

scientific article

Eppur si muove! The 2013 Nobel Prize in Chemistry

scientific article published in December 2013

Fluctuations and correlations in crystalline protein dynamics: a simulation analysis of staphylococcal nuclease

scientific article published on 28 January 2005

Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation

scientific article published in November 2003

Force field development and conformational search strategy in the simulation of biomolecular recognition processes

scientific article published on February 1996

Force-Field Development and Molecular Dynamics Simulations of Ferrocene–Peptide Conjugates as a Scaffold for Hydrogenase Mimics

article

GPCR6A is a Molecular Target for the Natural Products Gallate and EGCG in Green Tea.

scientific article published on 21 February 2018

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

scientific article

Glucose-6-phosphate dehydrogenase (G6PD) deficiency-type Zurich: a splice site mutation as an uncommon mechanism producing enzyme deficiency.

scientific article published in October 2004

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

scientific article

Hidden regularity and universal classification of fast side chain motions in proteins.

scientific article published on 6 June 2014

High-density hydration layer of lysozymes: molecular dynamics decomposition of solution scattering data.

scientific article

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

scientific article published on 04 April 2022

How random is a highly denatured protein?

scientific article published in December 1994

Hydration control of the mechanical and dynamical properties of cellulose.

scientific article published on 29 October 2014

Hydrogen-bond driven loop-closure kinetics in unfolded polypeptide chains

scientific article

Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers

scientific article

Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli.

scientific article published on 26 June 2017

Impact of resistance mutations on inhibitor binding to HIV-1 integrase

scientific article published on 21 November 2013

In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions

scientific article

Inelastic neutron scattering analysis of picosecond internal protein dynamics

article

Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism.

scientific article published in May 2006

Instantaneous normal modes and the protein glass transition

scientific article published on January 2009

Is the first hydration shell of lysozyme of higher density than bulk water?

scientific article

Key role of active-site water molecules in bacteriorhodopsin proton-transfer reactions

scientific article published in November 2008

Key role of electrostatic interactions in bacteriorhodopsin proton transfer

scientific article published in November 2004

L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study

scientific article

Langevin model of the temperature and hydration dependence of protein vibrational dynamics

scientific article published on 01 June 2005

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

scientific article

Lattice vibrations in crystalline L-alanine

scientific article published on 01 May 1993

Ligand-Dependent Sodium Ion Dynamics within the A2A Adenosine Receptor: A Molecular Dynamics Study

scientific article published on 12 September 2019

Liquid-like side-chain dynamics in myoglobin

scientific article published on 01 September 1994

Long-distance proton transfer with a break in the bacteriorhodopsin active site.

scientific article published on May 2009

Long-time mean-square displacements in proteins

scientific article published on 8 November 2013

Low-frequency vibrations in alpha-helices: helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories.

scientific article published in June 1995

Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k

scientific article published on 01 February 2006

Magnesium-dependent active-site conformational selection in the Diels-Alderase ribozyme

scientific article published on September 2010

Mechanical Properties of Nanoscopic Lipid Domains

article

Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides

scientific article published on 01 March 2010

Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States

scientific article published on 07 September 2014

Mechanism of DNA recognition by the restriction enzyme EcoRV.

scientific article published on 18 June 2010

Mechanism of Hg-C protonolysis in the organomercurial lyase MerB.

scientific article published in September 2009

Mechanism of a molecular valve in the halorhodopsin chloride pump

scientific article

Mechanism of lignin inhibition of enzymatic biomass deconstruction

scientific article

Mechanism of primary proton transfer in bacteriorhodopsin

scientific article published in July 2004

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

scientific article

Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II).

scientific article

Methyl group dynamics and the onset of anharmonicity in myoglobin

scientific article published on 10 April 2008

Molecular Dynamics Simulations of Proteins:  Can the Explicit Water Model Be Varied?

scientific article published on 01 July 2007

Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease

scientific article

Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching.

scientific article

Molecular origin of Gerstmann-Sträussler-Scheinker syndrome: insight from computer simulation of an amyloidogenic prion peptide.

scientific article

Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico.

scientific article

Motional displacements in proteins: The origin of wave-vector-dependent values

scientific article

Multi-conformer ensemble docking to difficult protein targets.

scientific article

Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum

scientific article (publication date: 16 August 2011)

Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins

scientific article published in October 2005

Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state

scientific article published in August 2009

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

scientific article

Organosolv-Water Cosolvent Phase Separation on Cellulose and its Influence on the Physical Deconstruction of Cellulose: A Molecular Dynamics Analysis

scientific article published on 3 November 2017

Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.

scientific article published on 27 October 2006

Oxidation of tetrahydro-beta-carboline by cytochrome P-450cam--determination and rationalisation of product distribution

scientific article published on 01 January 1998

Packing density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responses

scientific article published on 15 October 2008

Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae

scientific article

Partitioning of amino-acid analogues in a five-slab membrane model.

scientific article published on 28 June 2008

Peptide Partitioning and Folding into Lipid Bilayers

scientific article published on 01 September 2009

Peptide partitioning properties from direct insertion studies

scientific article published on June 2010

Pickin' Up Good Vibrations.

scientific article

Picosecond dynamical changes on denaturation of yeast phosphoglycerate kinase revealed by quasielastic neutron scattering.

scientific article published in July 1997

Picosecond fluctuating protein energy landscape mapped by pressure temperature molecular dynamics simulation

scholarly article

Picosecond timescale rigid-helix and side-chain motions in deoxymyoglobin.

scientific article published in June 1993

Polycystin-1 interacts with TAZ to stimulate osteoblastogenesis and inhibit adipogenesis

scientific article published on 27 November 2017

Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants

scientific article published on 3 August 2010

Protein dynamics and stability: the distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering

scientific article

Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns

scientific article published on 01 March 2007

Protein interactions and dynamics probed by quantum chemistry, computer simulations and neutron experiments.

scientific article published on December 1994

Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

scientific article published on 01 May 2005

Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins

scientific article published on 6 May 2017

Quasielastic neutron scattering in biology: Theory and applications

scientific article

REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

scientific article

REACH coarse-grained simulation of a cellulose fiber

scientific article published on 31 August 2012

Radical coupling reactions in lignin synthesis: a density functional theory study.

scientific article

Reconstruction of protein side-chain conformational free energy surfaces from NMR-derived methyl axis order parameters

scientific article published on 26 March 2012

Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions

scientific article published on 9 January 2018

Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations

scientific article

Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride.

scientific article published on 15 September 2014

Response of small-scale, methyl rotors to protein-ligand association: a simulation analysis of calmodulin-peptide binding

scientific article published on 01 July 2009

Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump.

scientific article published on 21 October 2016

Role of histone tails in structural stability of the nucleosome

scientific article

Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease

scientific article published on 05 August 2011

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

scientific article published in October 2009

Simulation analysis of the temperature dependence of lignin structure and dynamics

scientific article published on 28 November 2011

Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke

scientific article published on 30 June 2006

Soft collective fluctuations governing hydrophobic association

scientific article published on 18 September 2013

Solution structure of a putative HIV1 immunogenic peptide: computer simulation of the principal CD4 binding domain of gp120.

scientific article published in February 2002

Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation

scientific article published on 12 August 2008

Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes

scientific article published on 07 July 2014

Solvent-driven preferential association of lignin with regions of crystalline cellulose in molecular dynamics simulation

scientific article published on 26 September 2013

Stereoselection in the Diels-Alderase ribozyme: a molecular dynamics study

scientific article published on 02 May 2012

Structural and Functional Evidence for Testosterone Activation of GPRC6A in Peripheral Tissues

scientific article

Structural and energetic determinants of primary proton transfer in bacteriorhodopsin.

scientific article published on 4 April 2006

Structural basis of antibody cross-reactivity: solution conformation of an immunogenic peptide fragment containing both T and B epitopes

scientific article published on 01 October 1995

Structural basis of cellulosome efficiency explored by small angle X-ray scattering

scientific article published on 12 September 2005

Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase

scientific article published on 26 August 2011

Structural mechanism of the recovery stroke in the myosin molecular motor

scientific article

Structural model of the anti-snake-toxin antibody, M alpha 2,3.

scientific article published in September 1996

Structural model of the photosynthetic reaction center of Rhodobacter capsulatus

scientific article published on 01 July 1995

Structural modeling and molecular dynamics simulation of the actin filament

scientific article published on 09 May 2011

Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen

scientific article published on 01 February 1998

Structural modeling of the pro-ocytocin-neurophysin precursor

scientific article published on 01 October 1998

Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II).

scientific article published on 19 March 2010

Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase

scientific article

Structure and dynamics of bacteriorhodopsin. Comparison of simulation and experiment.

scientific article

Structure of human annexin I: comparison of homology modelling and crystallographic experiment

scientific article published on 01 November 1997

Structure of the Malpha2-3 toxin alpha antibody-antigen complex: combination of modelling with functional mapping experimental results

scientific article published on 01 May 2000

Structure-based design of broadly protective group a streptococcal M protein-based vaccines

scientific article published on 24 November 2016

Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations

scientific article

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

scientific article published on 16 December 2020

Supercomputing Pipelines Search for Therapeutics Against COVID-19

scientific article published on 06 November 2020

Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements

scientific article published on 20 October 2006

Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core

scientific article published on 05 June 2012

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers

scientific article published on 7 December 2010

Temperature and timescale dependence of protein dynamics in methanol : water mixtures

scientific article published in April 2005

Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein

scientific article published on 20 November 2012

Temperature-dependent protein dynamics: a simulation-based probabilistic diffusion-vibration Langevin description.

scientific article published in March 2006

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation

scientific article published on 11 October 2019

The alpha helix dipole: screened out?

scientific article published in June 2005

The dynamic transition in proteins may have a simple explanation.

scientific article

The influence of helix morphology on co-operative polyamide backbone conformational flexibility in peptide nucleic acid complexes

scientific article published in October 1999

The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor

scientific article published on 23 December 2006

The role of histone tails in the nucleosome: a computational study.

scientific article

The serotonin binding site of human and murine 5-HT2B receptors: molecular modeling and site-directed mutagenesis

scientific article (publication date: 10 May 2002)

The solvation structures of cellulose microfibrils in ionic liquids

scientific article published on 18 December 2011

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

scientific article published on 01 July 2007

The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations.

scientific article published on 16 January 2017

Theory and normal-mode analysis of change in protein vibrational dynamics on ligand binding

scientific article published in January 2010

Three entropic classes of side chain in a globular protein

scientific article

Tight in titin

scientific article published on 01 March 2006

Time-dependent density functional theory assessment of UV absorption of benzoic acid derivatives

scientific article published on 20 November 2012

Time-resolved computational protein biochemistry: solvent effects on interactions, conformational transitions and equilibrium fluctuations

scientific article published on 01 January 2003

Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins.

scientific article published in May 2006

Translational hydration water dynamics drives the protein glass transition

scientific article published on September 2003

Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues.

scientific article

Tuning of Retinal Twisting in Bacteriorhodopsin Controls the Directionality of the Early Photocycle Steps

scientific article published on 01 August 2005

Understanding the energetics of helical peptide orientation in membranes.

scientific article

Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study

scientific article published on 21 February 2012

Vibrational Softening of a Protein on Ligand Binding

article

VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers.

scientific article

Water pathways in the bacteriorhodopsin proton pump

scientific article published on 28 November 2010

Why Mercury Prefers Soft Ligands

article

Why genetic modification of lignin leads to low-recalcitrance biomass

scientific article

X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation

scientific article published in May 1998

X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and quantum mechanical/molecular mechanical study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs

scientific article

Zaccai neutron resilience and site-specific hydration dynamics in a globular protein

scientific article

de Gennes narrowing describes the relative motion of protein domains.

scientific article

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