Publications | David W. Wright

J. Dakka, M. Turilli, D. W. Wright, S. J Zasada, V. Balasubramanian, S. Wan, P. V. Coveney, S. Jha. High-throughput Binding Affinity Calculations at Extreme Scales. BMC Bioinformatics, 2018.

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D. W. Wright, S. Wan, C. Meyer, H. Van Vlijmen, G. Tresadern, P. V. Coveney. Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4. Chemrxiv, 2018.

Preprint

J. Dakka, K. Farkas-Pall, M. Turilli, D. W Wright, P. V Coveney, S. Jha. Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations. arXiv, 2018.

Preprint

W. Zhang, S. C. Howell, D. W. Wright, A. Heindel, X. Qiu, J. Chen, J. E. Curtis. Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates. Journal of Molecular Graphics & Modelling, 2017.

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N. A. Altwaijry, M. Baron, D. W. Wright, P. V. Coveney, A. 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, 2017.

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R. Nan, C. M Furze, D. W Wright, J. Gor, R. Wallis, S. J Perkins. Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation. Structure, 2017.

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A. P. Bhati, S. Wan, D. W. Wright, P. V. Coveney. Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration. Journal of Chemical Theory and Computation, 2017.

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K. Wai Fung, D. W Wright, J. Gor, M. J Swann, S. J Perkins. Domain structure of human complement C4b extends with increasing NaCl concentration: implications for its regulatory mechanism. Biochemical Journal, 2016.

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S. J. Perkins, D. W. Wright, H. Zhang, E. H. Brookes, J. Chen, T. C. Irving, S. Krueger, D. J. Barlow, K. J. Edler, D. J. Scott, N. J. Terrill, S. M. King, P. D. Butler, J. E. Curtis. Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS). Journal of Applied Crystallography, 2016.

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G. Kay Hui, D. W Wright, O. L Vennard, L. E Rayner, M. Pang, S. Cheng Yeo, J. Gor, K. Molyneux, J. Barratt, S. J Perkins. The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease. Biochemical Journal, 2015.

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J. B. Swadling, D. W. Wright, J. L. Suter, P. V. Coveney. Structure, Dynamics, and Function of the Hammerhead Ribozyme in Bulk Water and at a Clay Mineral Surface from Replica Exchange Molecular Dynamics. Langmuir, 2015.

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D. W Wright, S. J Perkins. SCT: a suite of programs for comparing atomistic models with small-angle scattering data. Journal of Applied Crystallography, 2015.

Code DOI Documentation

I. P Deuzing, C. Charpentier, D. W Wright, S. Matheron, J. Paton, D. Frentz, D. A van de Vijver, P. V Coveney, D. Descamps, C. A B Boucher, N. Beerens. Mutation V111I in HIV-2 Reverse Transcriptase Increases the Fitness of the Nucleoside Analogue-Resistant K65R and Q151M Viruses. Journal of Virology, 2015.

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J. M. Osborne, M. O. Bernabeu, M. Bruna, B. Calderhead, J. Cooper, N. Dalchau, S. Dunn, A. G. Fletcher, R. Freeman, D. Groen, B. Knapp, G. J. McInerny, G. R. Mirams, J. Pitt-Francis, B. Sengupta, D. W. Wright, C. A. Yates, D. J. Gavaghan, S. Emmott, C. Deane. Ten Simple Rules for Effective Computational Research. PLoS Computational Biology, 2014.

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D. W. Wright, B. A. Hall, O. A. Kenway, S. Jha, P. V. Coveney. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors. Journal of Chemical Theory and Computation, 2014.

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M. B A Kunze, D. W Wright, N. D Werbeck, J. Kirkpatrick, P. V Coveney, D. Flemming Hansen. Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8. Journal of the American Chemical Society, 2013.

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D. W Wright, I. P Deuzing, P. Flandre, P. van den Eede, M. Govaert, L. Setiawan, P. V Coveney, A. Marcelin, V. Calvez, C. A B Boucher, N. Beerens. A polymorphism at position 400 in the connection subdomain of HIV-1 reverse transcriptase affects sensitivity to NNRTIs and RNaseH activity. PLOS ONE, 2013.

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S. Wan, D. W Wright, P. V Coveney. Mechanism of Drug Efficacy Within the EGF Receptor Revealed by Microsecond Molecular Dynamics Simulation. Molecular Cancer Therapeutics, 2012.

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D. W Wright, S. Wan, N. Shublaq, S. J Zasada, P. V Coveney. From base pair to bedside: molecular simulation and the translation of genomics to personalized medicine. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2012.

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B. A Hall, D. W Wright, S. Jha, P. Vivian Coveney. Quantized water access to the HIV-1 protease active site as a proposed mechanism for cooperative mutations in drug affinity. Biochemistry, 2012.

D. W Wright, S. Kashif Sadiq, G. De Fabritiis, P. V Coveney. Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase. Journal of the American Chemical Society, 2012.

D. W. Wright, B. A. Hall, P. Kellam, P. V. Coveney. Global Conformational Dynamics of HIV-1 Reverse Transcriptase Bound to Non-Nucleoside Inhibitors. Biology, 2012.

D. W Wright, P. V Coveney. Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 2011.

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O. Kenway, D. W. Wright, H. Heller, A. Merzky, G. Pringle, J. Wolfrat, P. Coveney, S. Jha. Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences. Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG ‘11, 2011.

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S. Kashif Sadiq, D. W Wright, O. a Kenway, P. V Coveney. Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases. Journal of Chemical Information and Modeling, 2010.

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R. S Saksena, B. Boghosian, L. Fazendeiro, O. A Kenway, S. Manos, M. D Mazzeo, S. Kashif Sadiq, J. L Suter, D. Wright, P. V Coveney. Real science at the petascale. Philos. Trans. A Math Phys. Eng. Sci., 2009.

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S. Kashif Sadiq, D. Wright, S. J Watson, S. J Zasada, I. Stoica, P. V Coveney. Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases. Philos. Trans. A Math Phys. Eng. Sci., 2008.

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