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Uncertainty Quantification in Alchemical Free Energy Methods.

Bhati AP, Wan S, Hu Y, Sherborne B, Coveney PV.

J Chem Theory Comput. 2018 Apr 20. doi: 10.1021/acs.jctc.7b01143. [Epub ahead of print]


Graphene-Graphene Interactions: Friction, Superlubricity, and Exfoliation.

Sinclair RC, Suter JL, Coveney PV.

Adv Mater. 2018 Mar;30(13):e1705791. doi: 10.1002/adma.201705791. Epub 2018 Feb 13.


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

Eccleston RC, Coveney PV, Dalchau N.

Sci Rep. 2017 Oct 30;7(1):14367. doi: 10.1038/s41598-017-14415-8.


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

Eccleston RC, Wan S, Dalchau N, Coveney PV.

Front Immunol. 2017 Jul 10;8:797. doi: 10.3389/fimmu.2017.00797. eCollection 2017.


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

Altwaijry NA, Baron M, Wright DW, Coveney PV, Townsend-Nicholson A.

J Chem Theory Comput. 2017 May 9;13(5):2254-2270. doi: 10.1021/acs.jctc.6b01246. Epub 2017 Apr 25.


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

Wan S, Bhati AP, Skerratt S, Omoto K, Shanmugasundaram V, Bagal SK, Coveney PV.

J Chem Inf Model. 2017 Apr 24;57(4):897-909. doi: 10.1021/acs.jcim.6b00780. Epub 2017 Apr 4.


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

Wan S, Bhati AP, Zasada SJ, Wall I, Green D, Bamborough P, Coveney PV.

J Chem Theory Comput. 2017 Feb 14;13(2):784-795. doi: 10.1021/acs.jctc.6b00794. Epub 2017 Jan 18.


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

Bhati AP, Wan S, Wright DW, Coveney PV.

J Chem Theory Comput. 2017 Jan 10;13(1):210-222. doi: 10.1021/acs.jctc.6b00979. Epub 2016 Dec 20.


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

Coveney PV, Boon JP, Succi S.

Philos Trans A Math Phys Eng Sci. 2016 Nov 13;374(2080). pii: 20160335. No abstract available.


Big data need big theory too.

Coveney PV, Dougherty ER, Highfield RR.

Philos Trans A Math Phys Eng Sci. 2016 Nov 13;374(2080). pii: 20160153. Review.


On the calculation of equilibrium thermodynamic properties from molecular dynamics.

Coveney PV, Wan S.

Phys Chem Chem Phys. 2016 Nov 9;18(44):30236-30240.


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

Franco CA, Jones ML, Bernabeu MO, Vion AC, Barbacena P, Fan J, Mathivet T, Fonseca CG, Ragab A, Yamaguchi TP, Coveney PV, Lang RA, Gerhardt H.

Elife. 2016 Feb 4;5:e07727. doi: 10.7554/eLife.07727.


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

Bernabeu MO, Yang Lu, Lammer J, Aiello LP, Coveney PV, Sun JK.

Conf Proc IEEE Eng Med Biol Soc. 2015 Aug;2015:8070-3. doi: 10.1109/EMBC.2015.7320266.


Rapid, Precise, and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment.

Wan S, Knapp B, Wright DW, Deane CM, Coveney PV.

J Chem Theory Comput. 2015 Jul 14;11(7):3346-56. doi: 10.1021/acs.jctc.5b00179. Epub 2015 Jun 24.


Mechanism of Exfoliation and Prediction of Materials Properties of Clay-Polymer Nanocomposites from Multiscale Modeling.

Suter JL, Groen D, Coveney PV.

Nano Lett. 2015 Dec 9;15(12):8108-13. doi: 10.1021/acs.nanolett.5b03547. Epub 2015 Nov 24.


Computing the role of near attack conformations in an enzyme-catalyzed nucleophilic bimolecular reaction.

Sadiq SK, Coveney PV.

J Chem Theory Comput. 2015 Jan 13;11(1):316-24. doi: 10.1021/ct5008845. Epub 2014 Dec 2.


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

Bunney TD, Wan S, Thiyagarajan N, Sutto L, Williams SV, Ashford P, Koss H, Knowles MA, Gervasio FL, Coveney PV, Katan M.

EBioMedicine. 2015 Mar 1;2(3):194-204.


Correction: dynamic endothelial cell rearrangements drive developmental vessel regression.

Franco CA, Jones ML, Bernabeu MO, Geudens I, Mathivet T, Rosa A, Lopes FM, Lima AP, Ragab A, Collins RT, Phng LK, Coveney PV, Gerhardt H.

PLoS Biol. 2015 May 14;13(5):e1002163. doi: 10.1371/journal.pbio.1002163. eCollection 2015 May.


Dynamic endothelial cell rearrangements drive developmental vessel regression.

Franco CA, Jones ML, Bernabeu MO, Geudens I, Mathivet T, Rosa A, Lopes FM, Lima AP, Ragab A, Collins RT, Phng LK, Coveney PV, Gerhardt H.

PLoS Biol. 2015 Apr 17;13(4):e1002125. doi: 10.1371/journal.pbio.1002125. eCollection 2015 Apr. Erratum in: PLoS Biol. 2015 May;13(5):e1002163.


Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics.

Swadling JB, Wright DW, Suter JL, Coveney PV.

Langmuir. 2015 Mar 3;31(8):2493-501. doi: 10.1021/la503685t. Epub 2015 Feb 16.


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

Krüger T, Holmes D, Coveney PV.

Biomicrofluidics. 2014 Oct 13;8(5):054114. doi: 10.1063/1.4897913. eCollection 2014 Sep.


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

Deuzing IP, Charpentier C, Wright DW, Matheron S, Paton J, Frentz D, van de Vijver DA, Coveney PV, Descamps D; ANRS CO5 HIV-2 Cohort, Boucher CA, Beerens N.

J Virol. 2015 Jan;89(1):833-43. doi: 10.1128/JVI.02259-14. Epub 2014 Oct 29.


Choice of boundary condition for lattice-Boltzmann simulation of moderate-Reynolds-number flow in complex domains.

Nash RW, Carver HB, Bernabeu MO, Hetherington J, Groen D, Krüger T, Coveney PV.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Feb;89(2):023303. Epub 2014 Feb 18.


Detachment energies of spheroidal particles from fluid-fluid interfaces.

Davies GB, Krüger T, Coveney PV, Harting J.

J Chem Phys. 2014 Oct 21;141(15):154902. doi: 10.1063/1.4898071.


Assembling ellipsoidal particles at fluid interfaces using switchable dipolar capillary interactions.

Davies GB, Krüger T, Coveney PV, Harting J, Bresme F.

Adv Mater. 2014 Oct 22;26(39):6715-9. doi: 10.1002/adma.201402419. Epub 2014 Aug 13.


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

Bernabeu MO, Jones ML, Nielsen JH, Krüger T, Nash RW, Groen D, Schmieschek S, Hetherington J, Gerhardt H, Franco CA, Coveney PV.

J R Soc Interface. 2014 Oct 6;11(99). pii: 20140543. doi: 10.1098/rsif.2014.0543.


Interface deformations affect the orientation transition of magnetic ellipsoidal particles adsorbed at fluid-fluid interfaces.

Davies GB, Krüger T, Coveney PV, Harting J, Bresme F.

Soft Matter. 2014 Sep 21;10(35):6742-8. doi: 10.1039/c4sm01124d.


Performance of distributed multiscale simulations.

Borgdorff J, Ben Belgacem M, Bona-Casas C, Fazendeiro L, Groen D, Hoenen O, Mizeranschi A, Suter JL, Coster D, Coveney PV, Dubitzky W, Hoekstra AG, Strand P, Chopard B.

Philos Trans A Math Phys Eng Sci. 2014 Aug 6;372(2021). pii: 20130407. doi: 10.1098/rsta.2013.0407.


Multiscale modelling: approaches and challenges.

Karabasov S, Nerukh D, Hoekstra A, Chopard B, Coveney PV.

Philos Trans A Math Phys Eng Sci. 2014 Aug 6;372(2021). pii: 20130390. doi: 10.1098/rsta.2013.0390. No abstract available.


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

Wright DW, Hall BA, Kenway OA, Jha S, Coveney PV.

J Chem Theory Comput. 2014 Mar 11;10(3):1228-1241. Epub 2014 Jan 27.


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

Hunter P, Chapman T, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Shublaq N, Skår J, Stroetmann K, Tegner J, Thomas SR, Tollis I, Tsamardinos I, van Beek JH, Viceconti M.

Interface Focus. 2013 Apr 6;3(2):20130004. doi: 10.1098/rsfs.2013.0004.


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

Bernabeu MO, Nash RW, Groen D, Carver HB, Hetherington J, Krüger T, Coveney PV.

Interface Focus. 2013 Apr 6;3(2):20120094. doi: 10.1098/rsfs.2012.0094.


Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations.

Groen D, Borgdorff J, Bona-Casas C, Hetherington J, Nash RW, Zasada SJ, Saverchenko I, Mamonski M, Kurowski K, Bernabeu MO, Hoekstra AG, Coveney PV.

Interface Focus. 2013 Apr 6;3(2):20120087. doi: 10.1098/rsfs.2012.0087.


Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force.

Martin HS, Jha S, Coveney PV.

J Comput Chem. 2014 Apr 5;35(9):692-702. doi: 10.1002/jcc.23525. Epub 2014 Jan 9.


p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data.

Marés J, Shamardin L, Weiler G, Anguita A, Sfakianakis S, Neri E, Zasada SJ, Graf N, Coveney PV.

AMIA Annu Symp Proc. 2014 Nov 14;2014:872-81. eCollection 2014.


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

Kunze MB, Wright DW, Werbeck ND, Kirkpatrick J, Coveney PV, Hansen DF.

J Am Chem Soc. 2013 Nov 27;135(47):17862-8. doi: 10.1021/ja408184x. Epub 2013 Nov 15.


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

Wright DW, Deuzing IP, Flandre P, van den Eede P, Govaert M, Setiawan L, Coveney PV, Marcelin AG, Calvez V, Boucher CA, Beerens N.

PLoS One. 2013 Oct 2;8(10):e74078. doi: 10.1371/journal.pone.0074078. eCollection 2013.


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

Buchsbaum SF, Mitchell N, Martin H, Wiggin M, Marziali A, Coveney PV, Siwy Z, Howorka S.

Nano Lett. 2013 Aug 14;13(8):3890-6. doi: 10.1021/nl401968r. Epub 2013 Jul 10.


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

Könnyű B, Sadiq SK, Turányi T, Hírmondó R, Müller B, Kräusslich HG, Coveney PV, Müller V.

PLoS Comput Biol. 2013;9(6):e1003103. doi: 10.1371/journal.pcbi.1003103. Epub 2013 Jun 6.


Conformational effects on the pro-S hydrogen abstraction reaction in cyclooxygenase-1: an integrated QM/MM and MD study.

Christov CZ, Lodola A, Karabencheva-Christova TG, Wan S, Coveney PV, Mulholland AJ.

Biophys J. 2013 Mar 5;104(5):L5-7. doi: 10.1016/j.bpj.2013.01.040.


Influence of surface chemistry and charge on mineral-RNA interactions.

Swadling JB, Suter JL, Greenwell HC, Coveney PV.

Langmuir. 2013 Feb 5;29(5):1573-83. doi: 10.1021/la303352g. Epub 2013 Jan 24.


Regulation of JAK2 activation by Janus homology 2: evidence from molecular dynamics simulations.

Wan S, Coveney PV.

J Chem Inf Model. 2012 Nov 26;52(11):2992-3000. doi: 10.1021/ci300308g. Epub 2012 Oct 18.


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

Wright DW, Wan S, Shublaq N, Zasada SJ, Coveney PV.

Wiley Interdiscip Rev Syst Biol Med. 2012 Nov-Dec;4(6):585-98. doi: 10.1002/wsbm.1186. Epub 2012 Aug 15. Review.


Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity.

Hall BA, Wright DW, Jha S, Coveney PV.

Biochemistry. 2012 Aug 21;51(33):6487-9. doi: 10.1021/bi300432u. Epub 2012 Aug 8.


Mechanism of drug efficacy within the EGF receptor revealed by microsecond molecular dynamics simulation.

Wan S, Wright DW, Coveney PV.

Mol Cancer Ther. 2012 Nov;11(11):2394-400. doi: 10.1158/1535-7163.MCT-12-0644-T. Epub 2012 Aug 3.


Thumbs down for HIV: domain level rearrangements do occur in the NNRTI-bound HIV-1 reverse transcriptase.

Wright DW, Sadiq SK, De Fabritiis G, Coveney PV.

J Am Chem Soc. 2012 Aug 8;134(31):12885-8. doi: 10.1021/ja301565k. Epub 2012 Jul 30.


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

Shublaq N, Sansom C, Coveney PV.

Chem Biol Drug Des. 2013 Jan;81(1):5-12. doi: 10.1111/j.1747-0285.2012.01444.x. Review.


Confined cubic blue phases under shear.

Henrich O, Stratford K, Marenduzzo D, Coveney PV, Cates ME.

J Phys Condens Matter. 2012 Jul 18;24(28):284127. doi: 10.1088/0953-8984/24/28/284127. Epub 2012 Jun 27.


Theory, modelling and simulation in origins of life studies.

Coveney PV, Swadling JB, Wattis JA, Greenwell HC.

Chem Soc Rev. 2012 Aug 21;41(16):5430-46. doi: 10.1039/c2cs35018a. Epub 2012 Jun 7. Review.


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