List of works - Peter Coveney

A Comparison of the Bravyi-Kitaev and Jordan-Wigner Transformations for the Quantum Simulation of Quantum Chemistry

scientific article published on 02 October 2018

A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer

scientific article

A critical appraisal of polymer-clay nanocomposites.

scientific article

A polymorphism at position 400 in the connection subdomain of HIV-1 reverse transcriptase affects sensitivity to NNRTIs and RNaseH activity

scientific article (publication date: 2013)

A vision and strategy for the virtual physiological human in 2010 and beyond.

scientific article

A vision and strategy for the virtual physiological human: 2012 update.

scientific article published on April 2013

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility

scientific article published on 24 May 2022

An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics

scientific article published on 6 April 2017

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

scientific article published on 12 April 2019

Audited credential delegation: a usable security solution for the virtual physiological human toolkit

scientific article published on 30 March 2011

Big data need big theory too

scientific article

Big data: the end of the scientific method?

scientific article published on 01 April 2019

Bridging the gaps at the physics-chemistry-biology interface.

scientific article published on November 2016

Characterization of parafoveal hemodynamics associated with diabetic retinopathy with adaptive optics scanning laser ophthalmoscopy and computational fluid dynamics

scientific article published in August 2015

Chemically Specific Multiscale Modeling of the Shear-Induced Exfoliation of Clay-Polymer Nanocomposites

scientific article published on 15 June 2018

Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties.

scientific article

Computational biomedicine: a challenge for the twenty-first century

scientific article published on January 2012

Computational vaccinology: quantitative approaches

scientific article published on January 2003

Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis

scientific article

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.

scientific article published on 27 January 2014

Deformability-based red blood cell separation in deterministic lateral displacement devices-A simulation study ⬇️

scientific article

Detachment energies of spheroidal particles from fluid-fluid interfaces ⬇️

scientific article published on 01 October 2014

Disentangling steric and electrostatic factors in nanoscale transport through confined space.

scientific article

Dynamic endothelial cell rearrangements drive developmental vessel regression

scientific article

Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

scientific article published on 11 January 2019

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders

scientific article published on 26 April 2019

Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation

scientific article published on 19 July 2021

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

scientific article

Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer

scientific article

From Molecular Dynamics to Dissipative Particle Dynamics

scientific article

From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine.

scientific article published on 15 August 2012

Gag-Pol processing during HIV-1 virion maturation: a systems biology approach

scientific article (publication date: 2013)

Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors

scientific article

Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation

scientific article published on 13 February 2018

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

scientific article published on 16 October 2020

Host genotype and time dependent antigen presentation of viral peptides: predictions from theory.

scientific article published on 30 October 2017

Impact of blood rheology on wall shear stress in a model of the middle cerebral artery

scientific article

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

scientific article published on 16 March 2022

Large-scale binding affinity calculations on commodity compute clouds

scientific article published on 16 October 2020

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids.

scientific article

Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8.

scientific article

Merging genomic and phenomic data for research and clinical impact.

scientific article

Micromechanical exfoliation of graphene on the atomistic scale

scientific article published on 01 March 2019

Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold

scientific article published on 06 May 2019

Modelling biological complexity: a physical scientist's perspective

scientific article

Multiscale computing for science and engineering in the era of exascale performance

scientific article published on 01 April 2019

Multiscale modelling, simulation and computing: from the desktop to the exascale

scientific article published on 01 April 2019

Mutation V111I in HIV-2 reverse transcriptase increases the fitness of the nucleoside analogue-resistant K65R and Q151M viruses

scientific article

Non-canonical Wnt signalling modulates the endothelial shear stress flow sensor in vascular remodelling

scientific article published on 4 February 2016

On the usability of grid middleware and security mechanisms

scientific article published on August 2011

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

scientific article published in 2021

Patient-specific modelling in drug design, development and selection including its role in clinical decision-making

scientific article published on January 2013

Patient-specific simulation as a basis for clinical decision-making

scientific article

Petascale lattice-Boltzmann studies of amphiphilic cubic liquid crystalline materials in a globally distributed high-performance computing and visualization environment

scientific article published on August 2010

Principles Governing Control of Aggregation and Dispersion of Graphene and Graphene Oxide in Polymer Melts

scientific article published on 28 July 2020

Principles governing control of aggregation and dispersion of aqueous graphene oxide

scientific article published on 17 November 2021

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study.

scientific article published on 22 December 2016

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

scientific article

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

scientific article published on 20 December 2016

Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction

scientific article published on 16 October 2020

Reaction kinetics of catalyzed competitive heteropolymer cleavage.

scientific article published on 26 August 2011

Real science at the petascale.

scientific article

Scientific Grid computing

scientific article

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges ⬇️

scientific article published on November 3, 2010

TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing

scientific article published on 25 January 2021

The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study ⬇️

scientific article published on March 2015

The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition

scientific article

The heterogeneous multiscale method applied to inelastic polymer mechanics

scientific article published on 01 April 2019

The influence of base pair tautomerism on single point mutations in aqueous DNA

scientific article published on 16 October 2020

The virtual physiological human: building a framework for computational biomedicine I. Editorial

scientific article

Theory, modelling and simulation in origins of life studies

scientific article published on 07 June 2012

Towards blood flow in the virtual human: efficient self-coupling of HemeLB

scientific article published on 11 December 2020

Towards the design of new and improved drilling fluid additives using molecular dynamics simulations

scientific article published on March 2010

Uncertainty Quantification in Alchemical Free Energy Methods

scientific article published on 02 May 2018

VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations

scientific article published on 29 March 2021

List of works by Peter Coveney

A Comparison of the Bravyi-Kitaev and Jordan-Wigner Transformations for the Quantum Simulation of Quantum Chemistry

A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer

A critical appraisal of polymer-clay nanocomposites.

A polymorphism at position 400 in the connection subdomain of HIV-1 reverse transcriptase affects sensitivity to NNRTIs and RNaseH activity

A vision and strategy for the virtual physiological human in 2010 and beyond.

A vision and strategy for the virtual physiological human: 2012 update.

Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility

An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4

Audited credential delegation: a usable security solution for the virtual physiological human toolkit

Big data need big theory too

Big data: the end of the scientific method?

Bridging the gaps at the physics-chemistry-biology interface.

Characterization of parafoveal hemodynamics associated with diabetic retinopathy with adaptive optics scanning laser ophthalmoscopy and computational fluid dynamics

Chemically Specific Multiscale Modeling of the Shear-Induced Exfoliation of Clay-Polymer Nanocomposites

Chemically specific multiscale modeling of clay-polymer nanocomposites reveals intercalation dynamics, tactoid self-assembly and emergent materials properties.

Computational biomedicine: a challenge for the twenty-first century

Computational vaccinology: quantitative approaches

Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.

Deformability-based red blood cell separation in deterministic lateral displacement devices-A simulation study ⬇️

Detachment energies of spheroidal particles from fluid-fluid interfaces ⬇️

Disentangling steric and electrostatic factors in nanoscale transport through confined space.

Dynamic endothelial cell rearrangements drive developmental vessel regression

Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding

Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders

Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer

From Molecular Dynamics to Dissipative Particle Dynamics

From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine.

Gag-Pol processing during HIV-1 virion maturation: a systems biology approach

Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors

Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Host genotype and time dependent antigen presentation of viral peptides: predictions from theory.

Impact of blood rheology on wall shear stress in a model of the middle cerebral artery

Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Large-scale binding affinity calculations on commodity compute clouds

Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids.

Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8.

Merging genomic and phenomic data for research and clinical impact.

Micromechanical exfoliation of graphene on the atomistic scale

Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold

Modelling biological complexity: a physical scientist's perspective

Multiscale computing for science and engineering in the era of exascale performance

Multiscale modelling, simulation and computing: from the desktop to the exascale

Mutation V111I in HIV-2 reverse transcriptase increases the fitness of the nucleoside analogue-resistant K65R and Q151M viruses

Non-canonical Wnt signalling modulates the endothelial shear stress flow sensor in vascular remodelling

On the usability of grid middleware and security mechanisms

Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers

Patient-specific modelling in drug design, development and selection including its role in clinical decision-making

Patient-specific simulation as a basis for clinical decision-making

Petascale lattice-Boltzmann studies of amphiphilic cubic liquid crystalline materials in a globally distributed high-performance computing and visualization environment

Principles Governing Control of Aggregation and Dispersion of Graphene and Graphene Oxide in Polymer Melts

Principles governing control of aggregation and dispersion of aqueous graphene oxide

Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study.

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration

Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction

Reaction kinetics of catalyzed competitive heteropolymer cleavage.

Real science at the petascale.

Scientific Grid computing

T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges ⬇️

TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing

The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study ⬇️

The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition

The heterogeneous multiscale method applied to inelastic polymer mechanics

The influence of base pair tautomerism on single point mutations in aqueous DNA

The virtual physiological human: building a framework for computational biomedicine I. Editorial

Theory, modelling and simulation in origins of life studies

Towards blood flow in the virtual human: efficient self-coupling of HemeLB

Towards the design of new and improved drilling fluid additives using molecular dynamics simulations

Uncertainty Quantification in Alchemical Free Energy Methods

VECMAtk: a scalable verification, validation and uncertainty quantification toolkit for scientific simulations