Peter V Coveney (P V Coveney)

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 59

Top Topics

Convolutional Neural Network

Machine Learning

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

Interface focus

Journal of the Royal Society, Interface

This page only lists publications with an associated author ORCID identifier.

Publications

Sharp C Y Lo, Jon W S McCullough, Xiao Xue, Peter V Coveney
Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations. Journal of the Royal Society, Interface 21 (213) (2024)
Peter V Coveney, Roger Highfield
Artificial Intelligence Must Be Made More Scientific. Journal of chemical information and modeling 64 (15) (2024)
Sharp C Y Lo, Jon W S McCullough, Xiao Xue, Peter V Coveney
Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations. Journal of the Royal Society, Interface 21 (213) (2024)
Peter V Coveney, Roger Highfield
Artificial Intelligence Must Be Made More Scientific. Journal of chemical information and modeling 64 (15) (2024)
Peter V Coveney, Roger Highfield
Artificial Intelligence Must Be Made More Scientific. Journal of chemical information and modeling 64 (15) (2024)
Sharp C Y Lo, Jon W S McCullough, Xiao Xue, Peter V Coveney
Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations. Journal of the Royal Society, Interface 21 (213) (2024)
Peter V Coveney, Roger Highfield
Artificial Intelligence Must Be Made More Scientific. Journal of chemical information and modeling (2024)
Hannes H Loeffler, Shunzhou Wan, Marco Klähn, Agastya P Bhati, Peter V Coveney
Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations. Journal of chemical theory and computation (2024)
Sharp C Y Lo, Jon W S McCullough, Xiao Xue, Peter V Coveney
Uncertainty quantification of the impact of peripheral arterial disease on abdominal aortic aneurysms in blood flow simulations. Journal of the Royal Society, Interface 21 (213) (2024)
Katya Ahmad, Abid Javed, Conor Lanphere, Peter V Coveney, Elena V Orlova, Stefan Howorka
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nature communications 14 (1) (2023)
Mateusz K Bieniek, Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. Journal of chemical information and modeling 63 (3) (2023)
Tim Weaving, Alexis Ralli, William M Kirby, Andrew Tranter, Peter J Love, Peter V Coveney
A Stabilizer Framework for the Contextual Subspace Variational Quantum Eigensolver and the Noncontextual Projection Ansatz. Journal of chemical theory and computation (2023)
Mateusz K Bieniek, Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. Journal of chemical information and modeling 63 (3) (2023)
Agastya P Bhati, Art Hoti, Andrew Potterton, Mateusz K Bieniek, Peter V Coveney
Long Time Scale Ensemble Methods in Molecular Dynamics: Ligand-Protein Interactions and Allostery in SARS-CoV-2 Targets. Journal of chemical theory and computation (2023)
Shunzhou Wan, Agastya P Bhati, Peter V Coveney
Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions. Journal of chemical theory and computation (2023)
Mateusz K Bieniek, Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. Journal of chemical information and modeling 63 (3) (2023)
James L Suter, Peter V Coveney, Peter V Coveney
Large-Scale Molecular Dynamics Elucidates the Mechanics of Reinforcement in Graphene-Based Composites. Advanced materials (Deerfield Beach, Fla.) (2023)
Shunzhou Wan, Agastya P Bhati, Alexander D Wade, Peter V Coveney
Ensemble-Based Approaches Ensure Reliability and Reproducibility. Journal of chemical information and modeling (2023)
Mateusz K Bieniek, Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. Journal of chemical information and modeling (2023)
Tim Weaving, Alexis Ralli, William M Kirby, Andrew Tranter, Peter J Love, Peter V Coveney
A Stabilizer Framework for the Contextual Subspace Variational Quantum Eigensolver and the Noncontextual Projection Ansatz. Journal of chemical theory and computation 19 (3) (2023)
Mateusz K Bieniek, Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
TIES 2.0: A Dual-Topology Open Source Relative Binding Free Energy Builder with Web Portal. Journal of chemical information and modeling 63 (3) (2023)
Tim Weaving, Alexis Ralli, William M Kirby, Andrew Tranter, Peter J Love, Peter V Coveney
A Stabilizer Framework for the Contextual Subspace Variational Quantum Eigensolver and the Noncontextual Projection Ansatz. Journal of chemical theory and computation 19 (3) (2023)
Tim Weaving, Alexis Ralli, William M Kirby, Andrew Tranter, Peter J Love, Peter V Coveney
A Stabilizer Framework for the Contextual Subspace Variational Quantum Eigensolver and the Noncontextual Projection Ansatz. Journal of chemical theory and computation 19 (3) (2023)
Alexander D Wade, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility. Journal of chemical theory and computation 18 (6) (2022)
Dhriti Nepal, Saewon Kang, Katarina M Adstedt, Krishan Kanhaiya, Michael R Bockstaller, L Catherine Brinson, Markus J Buehler, Peter V Coveney, Kaushik Dayal, Jaafar A El-Awady, Luke C Henderson, David Lee Kaplan, Sinan Keten, Nicholas A Kotov, George C Schatz, Silvia Vignolini, Fritz Vollrath, Yusu Wang, Boris I Yakobson, Vladimir V Tsukruk, Hendrik Heinz
Hierarchically structured bioinspired nanocomposites. Nature materials (2022)
Shunzhou Wan, Agastya P Bhati, David W Wright, Ian D Wall, Alan P Graves, Darren Green, Peter V Coveney
Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors. Journal of chemical information and modeling 62 (10) (2022)
Peter V Coveney, Werner A Müller, James L Suter, Aravind Vijayaraghavan, Peter V Coveney
Mechanically Stable Ultrathin Layered Graphene Nanocomposites Alleviate Residual Interfacial Stresses: Implications for Nanoelectromechanical Systems. ACS applied nano materials 5 (12) (2022)
Peter V Coveney, Werner A Müller, James L Suter, Aravind Vijayaraghavan, Peter V Coveney
Mechanically Stable Ultrathin Layered Graphene Nanocomposites Alleviate Residual Interfacial Stresses: Implications for Nanoelectromechanical Systems. ACS applied nano materials 5 (12) (2022)
Agastya P Bhati, Peter V Coveney
Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols. Journal of chemical theory and computation 18 (4) (2022)
James L Suter, Peter V Coveney
Principles governing control of aggregation and dispersion of aqueous graphene oxide. Scientific reports 11 (1) (2021)
Alexander Gheorghiu, Peter V Coveney, Alya A Arabi
The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair. Physical chemistry chemical physics : PCCP 23 (10) (2021)
Mateusz K Bieniek, Agastya P Bhati, Shunzhou Wan, Peter V Coveney
TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing. Journal of chemical theory and computation 17 (2) (2021)
Maxime Vassaux, Shunzhou Wan, Wouter Edeling, Peter V Coveney
Ensembles Are Required to Handle Aleatoric and Parametric Uncertainty in Molecular Dynamics Simulation. Journal of chemical theory and computation 17 (8) (2021)
Agastya P Bhati, Shunzhou Wan, Dario Alfè, Austin R Clyde, Mathis Bode, Li Tan, Mikhail Titov, Andre Merzky, Matteo Turilli, Shantenu Jha, Roger R Highfield, Walter Rocchia, Nicola Scafuri, Sauro Succi, Dieter Kranzlmüller, Gerald Mathias, David Wifling, Yann Donon, Alberto Di Meglio, Sofia Vallecorsa, Heng Ma, Anda Trifan, Arvind Ramanathan, Tom Brettin, Alexander Partin, Fangfang Xia, Xiaotan Duan, Rick Stevens, Peter V Coveney
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers. Interface focus 11 (6) (2021)
Wouter Edeling, Hamid Arabnejad, Robbie Sinclair, Diana Suleimenova, Krishnakumar Gopalakrishnan, Bartosz Bosak, Derek Groen, Imran Mahmood, Daan Crommelin, Peter V Coveney
The impact of uncertainty on predictions of the CovidSim epidemiological code. Nature computational science 1 (2) (2021)
Shunzhou Wan, Agastya P Bhati, Alexander D Wade, Dario Alfè, Peter V Coveney
Thermodynamic and structural insights into the repurposing of drugs that bind to SARS-CoV-2 main protease. Molecular systems design & engineering 7 (2) (2021)
Tim Diederichs, Katya Ahmad, Jonathan R Burns, Quoc Hung Nguyen, Zuzanna S Siwy, Marc Tornow, Peter V Coveney, Robert Tampé, Stefan Howorka
Principles of Small-Molecule Transport through Synthetic Nanopores. ACS nano 15 (10) (2021)
Shunzhou Wan, Andrew Potterton, Fouad S Husseini, David W Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V Coveney
Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors. Interface focus 10 (6) (2020)
Shunzhou Wan, Agastya P Bhati, Stefan J Zasada, Peter V Coveney
Rapid, accurate, precise and reproducible ligand-protein binding free energy prediction. Interface focus 10 (6) (2020)
James L Suter, Robert C Sinclair, Peter V Coveney
Principles Governing Control of Aggregation and Dispersion of Graphene and Graphene Oxide in Polymer Melts. Advanced materials (Deerfield Beach, Fla.) 32 (36) (2020)
Alexander Gheorghiu, Peter V Coveney, Alya A Arabi
The influence of base pair tautomerism on single point mutations in aqueous DNA. Interface focus 10 (6) (2020)
Stefan J Zasada, David W Wright, Peter V Coveney
Large-scale binding affinity calculations on commodity compute clouds. Interface focus 10 (6) (2020)
Jon W S McCullough, Robin A Richardson, A Patronis, R Halver, R Marshall, M Ruefenacht, B J N Wylie, T Odaker, M Wiedemann, B Lloyd, E Neufeld, G Sutmann, A Skjellum, D Kranzlmüller, Peter V Coveney
Towards blood flow in the virtual human: efficient self-coupling of HemeLB. Interface focus 11 (1) (2020)
David W Wright, Fouad S Husseini, Shunzhou Wan, Christophe Meyer, Herman W T van Vlijmen, Gary John Tresadern, Peter V Coveney
Application of the ESMACS Binding Free Energy Protocol to a Multi-Binding Site Lactate Dehydogenase A Ligand Dataset. Advanced theory and simulations 3 (1) (2019)
Shunzhou Wan, Gary John Tresadern, Laura Perez Benito, Herman W T van Vlijmen, Peter V Coveney
Accuracy and Precision of Alchemical Relative Free Energy Predictions with and without Replica-Exchange. Advanced theory and simulations 3 (1) (2019)
Agastya P Bhati, Shunzhou Wan, Peter V Coveney
Ensemble-Based Replica Exchange Alchemical Free Energy Methods: The Effect of Protein Mutations on Inhibitor Binding. Journal of chemical theory and computation 15 (2) (2019)
Robert C Sinclair, Peter V Coveney
Modeling Nanostructure in Graphene Oxide: Inhomogeneity and the Percolation Threshold. Journal of chemical information and modeling 59 (6) (2019)
David W Wright, Shunzhou Wan, Christophe Meyer, Herman W T van Vlijmen, Gary John Tresadern, Peter V Coveney
Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4. Scientific reports 9 (1) (2019)
Andrew Potterton, Fouad S Husseini, Michelle W Y Southey, Mike J Bodkin, Alexander Heifetz, Peter V Coveney, Andrea Townsend-Nicholson
Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A2A Receptor Binders. Journal of chemical theory and computation 15 (5) (2019)
Robert C Sinclair, James L Suter, Peter V Coveney
Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation. Advanced materials (Deerfield Beach, Fla.) 30 (13) (2018)
Agastya P Bhati, Shunzhou Wan, Yuan Hu, Brad Sherborne, Peter V Coveney
Uncertainty Quantification in Alchemical Free Energy Methods. Journal of chemical theory and computation 14 (6) (2018)
Andrew Tranter, Peter J Love, Florian Mintert, Peter V Coveney
A Comparison of the Bravyi-Kitaev and Jordan-Wigner Transformations for the Quantum Simulation of Quantum Chemistry. Journal of chemical theory and computation 14 (11) (2018)
R Charlotte Eccleston, Peter V Coveney, Neil Dalchau
Host genotype and time dependent antigen presentation of viral peptides: predictions from theory. Scientific reports 7 (1) (2017)
Shunzhou Wan, Agastya P Bhati, Stefan J Zasada, Ian Wall, Darren Green, Paul Bamborough, Peter V Coveney
Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study. Journal of chemical theory and computation 13 (2) (2017)
Peter V Coveney, Edward R Dougherty, Roger R Highfield
Big data need big theory too. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 374 (2080) (2017)
Nojood A Altwaijry, Michael Baron, David W Wright, Peter V Coveney, Andrea Townsend-Nicholson
An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics. Journal of chemical theory and computation 13 (5) (2017)
Shunzhou Wan, Agastya P Bhati, Sarah Skerratt, Kiyoyuki Omoto, Veerabahu Shanmugasundaram, Sharan K Bagal, Peter V Coveney
Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation. Journal of chemical information and modeling 57 (4) (2017)
Peter V Coveney, J P Boon, S Succi
Bridging the gaps at the physics-chemistry-biology interface. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 374 (2080) (2017)
Agastya P Bhati, Shunzhou Wan, David W Wright, Peter V Coveney
Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration. Journal of chemical theory and computation 13 (1) (2016)
Timm Krüger, David Holmes, Peter V Coveney
Deformability-based red blood cell separation in deterministic lateral displacement devices-A simulation study. Biomicrofluidics 8 (5) (2014)