Peter V Coveney

Summary

Affiliation: University College London
Country: UK

Publications

  1. doi request reprint Theory, modelling and simulation in origins of life studies
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
    Chem Soc Rev 41:5430-46. 2012
  2. ncbi request reprint Computational biomedicine: a challenge for the twenty-first century
    Peter V Coveney
    Centre for Computational Science, University College London, United Kingdom
    Stud Health Technol Inform 174:105-10. 2012
  3. pmc T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges
    Darren R Flower
    Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
    Immunome Res 6:S4. 2010
  4. pmc Modelling biological complexity: a physical scientist's perspective
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, UK
    J R Soc Interface 2:267-80. 2005
  5. ncbi request reprint Self-organization and complexity: a new age for theory, computation and experiment
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Philos Trans A Math Phys Eng Sci 361:1057-79. 2003
  6. ncbi request reprint WEDS: a Web services-based environment for distributed simulation
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, London, UK
    Philos Trans A Math Phys Eng Sci 363:1807-16. 2005
  7. ncbi request reprint Scientific Grid computing
    Peter V Coveney
    Centre for Computational Science and Department of Chemistry, University College London, UK
    Philos Trans A Math Phys Eng Sci 363:1707-13. 2005
  8. doi request reprint Role of host layer flexibility in DNA guest intercalation revealed by computer simulation of layered nanomaterials
    Mary Ann Thyveetil
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
    J Am Chem Soc 130:12485-95. 2008
  9. ncbi request reprint Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, UK
    Philos Transact A Math Phys Eng Sci 363:2037-53. 2005
  10. doi request reprint Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases
    S Kashif Sadiq
    Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK
    J Chem Inf Model 48:1909-19. 2008

Collaborators

Detail Information

Publications50

  1. doi request reprint Theory, modelling and simulation in origins of life studies
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, UCL, 20 Gordon Street, London, WC1H 0AJ, UK
    Chem Soc Rev 41:5430-46. 2012
    ..We then discuss state-of-the-art computationally-based molecular modelling techniques that are currently being deployed to investigate various scenarios relevant to the origins of life...
  2. ncbi request reprint Computational biomedicine: a challenge for the twenty-first century
    Peter V Coveney
    Centre for Computational Science, University College London, United Kingdom
    Stud Health Technol Inform 174:105-10. 2012
    ..They make demands of information technology at many scales, from the desktop to national and international infrastructures for data storage and processing, linked by high performance networks...
  3. pmc T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges
    Darren R Flower
    Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
    Immunome Res 6:S4. 2010
    ..We exemplify this within the context of immunoinformatics...
  4. pmc Modelling biological complexity: a physical scientist's perspective
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, UK
    J R Soc Interface 2:267-80. 2005
    ....
  5. ncbi request reprint Self-organization and complexity: a new age for theory, computation and experiment
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Philos Trans A Math Phys Eng Sci 361:1057-79. 2003
    ..Finally, I discuss how the advent of computational grids is set to provide a major boost to the study of such complex, self-organizing systems...
  6. ncbi request reprint WEDS: a Web services-based environment for distributed simulation
    Peter V Coveney
    Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, London, UK
    Philos Trans A Math Phys Eng Sci 363:1807-16. 2005
    ....
  7. ncbi request reprint Scientific Grid computing
    Peter V Coveney
    Centre for Computational Science and Department of Chemistry, University College London, UK
    Philos Trans A Math Phys Eng Sci 363:1707-13. 2005
    ..We review science that has been enabled by contemporary computational Grids, and associated progress made through the widening availability of high performance computing...
  8. doi request reprint Role of host layer flexibility in DNA guest intercalation revealed by computer simulation of layered nanomaterials
    Mary Ann Thyveetil
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
    J Am Chem Soc 130:12485-95. 2008
    ....
  9. ncbi request reprint Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, UK
    Philos Transact A Math Phys Eng Sci 363:2037-53. 2005
    ..The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines...
  10. doi request reprint Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases
    S Kashif Sadiq
    Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK
    J Chem Inf Model 48:1909-19. 2008
    ..Such a timescale is of direct clinical relevance and can assist in decision support for the assessment of patient-specific optimal drug treatment and the subsequent response to therapy for any given genotype...
  11. ncbi request reprint Lattice Boltzmann simulation of the flow of binary immiscible fluids with different viscosities using the Shan-Chen microscopic interaction model
    Jonathan Chin
    Centre for Computational Science, Queen Mary, University of London, UK
    Philos Trans A Math Phys Eng Sci 360:547-58. 2002
    ..Although a finger-like structure was observed in many simulations, it is not clear if this structure was produced due to viscous fingering or due to other effects...
  12. doi request reprint Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases
    S Kashif Sadiq
    Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, United Kingdom
    J Chem Inf Model 50:890-905. 2010
    ..This level of performance promotes integration of such methodology with clinical decision support systems for the optimization of patient-specific therapy...
  13. doi request reprint Mechanism of drug efficacy within the EGF receptor revealed by microsecond molecular dynamics simulation
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, WC1H 0AJ, United Kingdom
    Mol Cancer Ther 11:2394-400. 2012
    ....
  14. ncbi request reprint Molecular dynamics simulations: bring biomolecular structures alive on a computer
    Shunzhou Wan
    Centre for Computational Science, Chemistry Department, University College of London, UK
    Methods Mol Biol 409:321-39. 2007
    ..In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation...
  15. doi request reprint Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
    Ileana Stoica
    Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AH, UK
    J Am Chem Soc 130:2639-48. 2008
    ....
  16. ncbi request reprint Three-dimensional hydrodynamic lattice-gas simulations of ternary amphiphilic fluids under shear flow
    Peter J Love
    Centre for Computational Science, Queen Mary, University of London, UK
    Philos Trans A Math Phys Eng Sci 360:357-66. 2002
    ..The effect of micellization on interfacial behaviour in these phases is discussed in the context of the linear non-equilibrium thermodynamic theory of rate processes and nonlinear Becker-Döring aggregation theory...
  17. ncbi request reprint Hybrid molecular-continuum fluid models: implementation within a general coupling framework
    Rafael Delgado-Buscalioni
    Centre for Computational Science, Department of Chemistry, University College London, UK
    Philos Transact A Math Phys Eng Sci 363:1975-85. 2005
    ..Here we describe the implementation of our HybridMD code within a coupling framework that facilitates flexible deployment on such architectures...
  18. doi request reprint Influence of surface chemistry and charge on mineral-RNA interactions
    Jacob B Swadling
    The Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom
    Langmuir 29:1573-83. 2013
    ..An observation pertinent to the role of these minerals in prebiotic chemistry is that, for a given charge density on the mineral surface, different genetic sequences of RNA adopt different configurations...
  19. doi request reprint Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity
    Benjamin A Hall
    Centre for Computational Science, Department of Chemistry, UCL, London, UK
    Biochemistry 51:6487-9. 2012
    ..We propose that individual mutations induce changes in flap packing that are insufficient to allow water binding but in combination allow access, leading to the observed cooperative resistance...
  20. doi request reprint Patient-specific simulation as a basis for clinical decision-making
    S Kashif Sadiq
    Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
    Philos Transact A Math Phys Eng Sci 366:3199-219. 2008
    ..We describe systems that enable such priority computing...
  21. ncbi request reprint Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance
    Fabrizio Giordanetto
    Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, UK
    Philos Transact A Math Phys Eng Sci 363:2055-73. 2005
    ..Our simulations, therefore, provide insight into the molecular basis for drug resistance with S. pneumoniae DHPS...
  22. doi request reprint A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, London WC1A 0HE, United Kingdom
    J Comput Chem 30:1038-50. 2009
    ....
  23. doi request reprint Computer simulation study of the structural stability and materials properties of DNA-intercalated layered double hydroxides
    Mary Ann Thyveetil
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
    J Am Chem Soc 130:4742-56. 2008
    ..We also discuss how the materials properties of the LDH are modified due to DNA intercalation...
  24. doi request reprint Resolution of discordant HIV-1 protease resistance rankings using molecular dynamics simulations
    David W Wright
    Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
    J Chem Inf Model 51:2636-49. 2011
    ....
  25. ncbi request reprint Toward an atomistic understanding of the immune synapse: large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Mol Immunol 45:1221-30. 2008
    ..Multi-scale molecular dynamics simulations may be the best opportunity we have to reach a full understanding of this remarkable supra-macromolecular event at a cell-cell junction...
  26. ncbi request reprint Grid-based steered thermodynamic integration accelerates the calculation of binding free energies
    Philip W Fowler
    Centre for Computational Science, Department of Chemistry, University College London, Christopher Ingold Laboratories, UK
    Philos Transact A Math Phys Eng Sci 363:1999-2015. 2005
    ..Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach...
  27. doi request reprint Molecular dynamics simulation reveals structural and thermodynamic features of kinase activation by cancer mutations within the epidermal growth factor receptor
    Shunzhou Wan
    Department of Chemistry, Centre for Computational Science, University College London, London WC1H 0AJ, United Kingdom
    J Comput Chem 32:2843-52. 2011
    ..Our study reveals that the L834R mutation introduces conformational changes in both states, adjusting the relative stabilities of active and inactive conformations and hence the activation of the EGFR kinase...
  28. doi request reprint Regulation of JAK2 activation by Janus homology 2: evidence from molecular dynamics simulations
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
    J Chem Inf Model 52:2992-3000. 2012
    ..Thus abrogation of the domain-domain interaction seems to be a possible first step for the structural rearrangement of the two domains, resulting in constitutive activation of JAK2 by the V617F mutation...
  29. doi request reprint Patient-specific modelling in drug design, development and selection including its role in clinical decision-making
    Nour Shublaq
    Centre for Computational Science and Computational Life and Medical Sciences Network, University College London, London, UK
    Chem Biol Drug Des 81:5-12. 2013
    ..Investment in computational infrastructure is needed so that results can be returned on clinically relevant timescales and data warehouses designed with data protection as well as accessibility in mind...
  30. doi request reprint From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine
    David W Wright
    Centre for Computational Science, University College London, London, UK
    Wiley Interdiscip Rev Syst Biol Med 4:585-98. 2012
    ....
  31. ncbi request reprint Multiscale dissipative particle dynamics
    Gianni De Fabritiis
    Centre for Computational Science, Queen Mary, University of London, UK
    Philos Trans A Math Phys Eng Sci 360:317-31. 2002
    ..The main features of this DPD method are the adaptivity of the dissipative particles to the important length-scales of the problem and the explicit role played by the molecular pair-distribution function...
  32. ncbi request reprint Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site
    S Kashif Sadiq
    Centre for Computational Science, Department of Chemistry, University College London, London, WC1H 0AJ, UK
    Biochemistry 46:14865-77. 2007
    ..Finally, unidirectional translation may be countered by designing inhibitors with terminal subsites that provide sufficient anchoring to the flaps, thus increasing the steric barrier for translation in either direction...
  33. ncbi request reprint Real science at the petascale
    Radhika S Saksena
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Philos Transact A Math Phys Eng Sci 367:2557-71. 2009
    ....
  34. ncbi request reprint Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules
    G Giupponi
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London, UK
    J Chem Phys 126:154903. 2007
    ....
  35. ncbi request reprint Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer
    Shantenu Jha
    Centre for Computational Science, University College London, London WC1H 0AJ, United Kingdom
    J Comput Chem 26:1617-27. 2005
    ..This sets the stage for reliable large-scale simulations of nucleic acids using NAMD...
  36. ncbi request reprint Merging genomic and phenomic data for research and clinical impact
    Nour W Shublaq
    Centre for Computational Science, University College London, United Kingdom
    Stud Health Technol Inform 174:111-5. 2012
    ..S. $100. We discuss some of the issues that will need to be addressed by society as a result of this revolution in healthcare...
  37. doi request reprint Clay minerals mediate folding and regioselective interactions of RNA: a large-scale atomistic simulation study
    Jacob B Swadling
    Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
    J Am Chem Soc 132:13750-64. 2010
    ....
  38. pmc A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer
    Philip W Fowler
    Centre for Computational Science, Department of Chemistry, University College London, London, United Kingdom
    Biophys J 91:401-10. 2006
    ..These interactions stabilize the system and are similar to interactions observed for transmembrane proteins...
  39. pmc Audited credential delegation: a usable security solution for the virtual physiological human toolkit
    Ali N Haidar
    Centre for Computational Science, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Interface Focus 1:462-73. 2011
    ....
  40. pmc Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
    Shunzhou Wan
    Centre for Computational Science, Chemistry Department, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    J R Soc Interface 8:1114-27. 2011
    ....
  41. ncbi request reprint Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing
    Shunzhou Wan
    Centre for Computational Science, Department of Chemistry, University College London, United Kingdom
    J Immunol 175:1715-23. 2005
    ..This enables us to simulate larger, more realistic biological systems for longer durations without the imposition of artificial constraints...
  42. ncbi request reprint Layered double hydroxide minerals as possible prebiotic information storage and transfer compounds
    H Chris Greenwell
    Centre for Computational Science, Christopher Ingold Laboratory, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
    Orig Life Evol Biosph 36:13-37. 2006
    ....
  43. ncbi request reprint Towards the design of new and improved drilling fluid additives using molecular dynamics simulations
    Richard L Anderson
    Department of Chemistry, Durham University, Durham, United Kingdom
    An Acad Bras Cienc 82:43-60. 2010
    ..The structure and interactions of poly(propylene oxide)-diamine, poly(ethylene glycol) and poly(ethylene oxide)-diacrylate inhibitor molecules with montmorillonite clay are studied...
  44. ncbi request reprint On the usability of grid middleware and security mechanisms
    Stefan J Zasada
    Centre for Computational Science, University College London, 20 Gordon Street, London WC1H 0AJ, UK
    Philos Transact A Math Phys Eng Sci 369:3413-28. 2011
    ..Our middleware and security solutions are judged to be more usable than the systems in use by most of today's computational grids...
  45. ncbi request reprint Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids
    Jens Harting
    Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
    Philos Transact A Math Phys Eng Sci 363:1895-915. 2005
    ..The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organization of liquid cubic mesophases...
  46. ncbi request reprint Computational vaccinology: quantitative approaches
    Darren R Flower
    Edward Jenner Institute for Vaccine Research, High Street, Compton, Berkshire, RG0 7NN, UK
    Novartis Found Symp 254:102-20; discussion 120-5, 216-22, 250-2. 2003
    ..Both methods are exemplified through their application to the well-studied problem of peptide binding to the human class I MHC molecule HLA-A*0201...
  47. ncbi request reprint Symmetry-breaking in chiral polymerisation
    Jonathan A D Wattis
    Theoretical Mechanics, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
    Orig Life Evol Biosph 35:243-73. 2005
    ..The system then approaches one of the steady-state solutions described above...
  48. ncbi request reprint Monotopic enzymes and lipid bilayers: a comparative study
    Philip W Fowler
    Department of Biochemistry, University of Oxford, UK
    Biochemistry 46:3108-15. 2007
    ..Our results support these models and suggest that basic residues contribute significantly to the binding of these monotopic proteins to bilayers through the formation of hydrogen bonds with phospholipids...
  49. doi request reprint The virtual physiological human: building a framework for computational biomedicine I. Editorial
    Gordon Clapworthy
    Philos Transact A Math Phys Eng Sci 366:2975-8. 2008
  50. ncbi request reprint Developmental and physiological circuits: dissecting complexity. A report on a talk given by Dr Leroy Hood
    John Skår
    Karolinska Institutet, 171 77 Stockholm, Sweden
    Philos Transact A Math Phys Eng Sci 361:1313-7. 2003
    ..Dr Leroy Hood, the President and Director of the Institute for Systems Biology in Seattle, WA, USA, also spoke at the Nobel Symposium on self-organization. The main points of his talk are summarized in this paper...