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Molecular dynamics simulation reveals structural and thermodynamic features of kinase activation by cancer mutations within the epidermal growth factor receptor.
Wan S, Coveney PV. Wan S, et al. Among authors: coveney pv. J Comput Chem. 2011 Oct;32(13):2843-52. doi: 10.1002/jcc.21866. Epub 2011 Jun 30. J Comput Chem. 2011. PMID: 21717480
Comparison of molecular dynamics with hybrid continuum-molecular dynamics for a single tethered polymer in a solvent.
Barsky S, Delgado-Buscalioni R, Coveney PV. Barsky S, et al. Among authors: coveney pv. J Chem Phys. 2004 Aug 1;121(5):2403-11. doi: 10.1063/1.1767996. J Chem Phys. 2004. PMID: 15260795
Hybrid molecular-continuum fluid dynamics.
Delgado-Buscalioni R, Coveney PV. Delgado-Buscalioni R, et al. Among authors: coveney pv. Philos Trans A Math Phys Eng Sci. 2004 Aug 15;362(1821):1639-54. doi: 10.1098/rsta.2004.1401. Philos Trans A Math Phys Eng Sci. 2004. PMID: 15306436
Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: can the alpha3 and beta2m domains be neglected?
Wan S, Coveney P, Flower DR. Wan S, et al. J Comput Chem. 2004 Nov 30;25(15):1803-13. doi: 10.1002/jcc.20100. J Comput Chem. 2004. PMID: 15386470
Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing.
Wan S, Coveney PV, Flower DR. Wan S, et al. Among authors: coveney pv. J Immunol. 2005 Aug 1;175(3):1715-23. doi: 10.4049/jimmunol.175.3.1715. J Immunol. 2005. PMID: 16034112
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies.
Fowler PW, Jha S, Coveney PV. Fowler PW, et al. Among authors: coveney pv. Philos Trans A Math Phys Eng Sci. 2005 Aug 15;363(1833):1999-2015. doi: 10.1098/rsta.2005.1625. Philos Trans A Math Phys Eng Sci. 2005. PMID: 16099763
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations.
Wan S, Coveney PV, Flower DR. Wan S, et al. Among authors: coveney pv. Philos Trans A Math Phys Eng Sci. 2005 Aug 15;363(1833):2037-53. doi: 10.1098/rsta.2005.1627. Philos Trans A Math Phys Eng Sci. 2005. PMID: 16099765
Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance.
Giordanetto F, Fowler PW, Saqi M, Coveney PV. Giordanetto F, et al. Among authors: coveney pv. Philos Trans A Math Phys Eng Sci. 2005 Aug 15;363(1833):2055-73. doi: 10.1098/rsta.2005.1629. Philos Trans A Math Phys Eng Sci. 2005. PMID: 16099766
Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer.
Jha S, Coveney PV, Laughton CA. Jha S, et al. Among authors: coveney pv. J Comput Chem. 2005 Nov 30;26(15):1617-27. doi: 10.1002/jcc.20300. J Comput Chem. 2005. PMID: 16170796
Hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules.
Giupponi G, De Fabritiis G, Coveney PV. Giupponi G, et al. Among authors: coveney pv. J Chem Phys. 2007 Apr 21;126(15):154903. doi: 10.1063/1.2720385. J Chem Phys. 2007. PMID: 17461663
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