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Haworth, N. L., Wang, Q., Coote, M. L. (2017) Modelling flexible molecules in Solution: A pKa Case Study, The Journal Physical Chemistry A, 121 (27): 5217–5225. DOI: 10.1021/acs.jpca.7b04133

Knapp, B., Alcala, M., Zhang, H., West, C. E., van der Merwe, P. A., Deane, C. M. (2017) pyHVis3D: Visualising Molecular Simulation Deduced H-bond Networks in 3D: Application to T-cell Receptor Interactions, Bioinformatics, btx842, DOI:

Langley, G. W., Brinkø, A., Munzel, M., Walport, L. J., Schofield, C. J., Hopkinson, R. J. (2017) Probing the Charge and Conformational Requirements of JmjC Demethylases, The FASEB Journal, vol. 31 no. 1, Supplement 767.1

Lei, C. L., Wang, K., Clerx, M., Johnstone, R.H, Hortigon-Vinagre, M. P., Zamora, V., Allan, A., Smith, G. L., Gavaghan, D. J., Mirams, G. R., Polonchuck, L. (2017) Tailoring Mathematical Models to Stem-Cell Derived Cardiomyocyte Lines Can Improve Predictions of Drug-Induced Changes to Their Electrophysiology, Frontiers in Physiology, 8, Article: 986. DOI:

Marks, C., Nowak, J., Klostermann, S., Georges, G., Dunbar, J., Shi, J., Kelm, S., Deane, C. M., (2017) Sphinx: Merging Knowledge-Based and Ab Initio Approaches to Improve Protein Loop Prediction, Bioinformatics, 33: 1346-1353. DOI: 10.1093/bioinformatics/btw823

Mazer, N. A., Hutton-Smith, L. A., Byrne, H. M., Gaffney, E. A., Maini, P. K., Gadkar, K. (2017) What Determines the Retinal Concentration of an Intravitreally Injected Antibody? New Insights Using a 3-Compartment Semi Mechanistic Pharmacokinetic Model, Conference Publication, ARVO Annual Meeting Abstract, Vol. 58, No. 8.

Parks, T., Mirabel, M. M., Kado, J., Auckland, K., Nowak, J., Rautanen, A., Mentzer, A. J., Marijon, E., Jouven, X., Perman, M. L., Cua, T., Kauwe, J. K., Allen, J. B., Taylor, H., Robson, K. J., Deane, C. M., Steer, A. C., Hill, A. V. S. (2017) Association between a Common Immunoglobulin Heavy Chain Allele and Rheumatic Heart Disease Risk in Oceania, Nature Communications, 8, 14946. DOI: 10.1038/ncomms14946

Regep, C., Georges, G., Shi, J., Popovic, B. & Deane, C. M. (2017) The H3 Loop of Antibodies Shows Unique Structural Characteristics, Proteins Structure Function and Bioinformatics, 85(7):1311-1318, DOI: 10.1002/prot.25291

Schuller, M., Höfner, G., Wanner, K. T. (2017) Simultaneous Multiple MS Binding Assays addressing D1 and D2 Dopamine receptors, ChemMedChem, 12(19):1585-1594. DOI: 10.1002/cmdc.201700369

Schuller, M., Riedel, K., Gibbs-Seymour, I., Uth, K., Sieg, C., Gehring, A. P., Ahel, I., Bracher, F., Kessler, B. M., Elkins, J. M., Knapp, S. (2017) Discovery of a Selective Allosteric Inhibitor Targeting Macrodomain 2 of Poly-Adenosine-Diphosphate-Ribose Polymerase 14, ACS Chemical Biology, 2(11):2866-2874. DOI: 10.1021/acschembio.7b00445

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Hutton-Smith, L. A., Gaffney, E. A., Byrne, H. M., Maini, P. K., Gadkar, K., Mazer, N. A. (2017) Ocular Pharmacokinetics of Therapeutic Antibodies Given by Intravitreal Injection: Estimation of Retinal Permeabilities Using a 3 Compartment Semi-Mechanistic Model, Molecular Pharmaceutics, 14(8):2690-2696. DOI: 10.1021/acs.molpharmaceut.7b00164




Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., Biggin, P. C. (2016) Accurate Calculation of the Absolute Free Energy of Binding for Drug Molecules, Chemical Science, 7(1):207-218. DOI: 10.1039/C5SC02678D

Cox, O., Krojer, T., Collins, P., Monteiro, O., Talon, R., Bradley, A., Fedorov, O., Amin, J., Marsden, B., Spencer, J., von Delft, F., Brennan, P. (2016) A Poised Fragment Library Enables Rapid Synthetic Expansion Yielding the First Reported Inhibitors Of PHIP(2), an Atypical Bromodomain, Chemical Science, 7:2322-2330. DOI: 10.1039/C5SC03115J

Dunbar, J., Krawczyk, K., Leem, J., Marks, C., Nowak, J., Regep, C., Georges, G., Kelm, L., Popovic, B., Deane, C. M. (2016). Sabpred: A Structure-Based Antibody Prediction Server, Nucleic Acids Research, 44(W1):W474-8. DOI: 10.1093/nar/gkw361

Heifetz, A., Chudyk, E., Gleave, L., Aldeghi, M., Cherezov, V., Fedorov, D., Biggin, P., Bodkin, M. (2016) The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR-Ligand Interactions, Journal of Chemical Information and Modeling, 25;56(1):159-72. DOI: 10.1021/acs.jcim.5b00644

Heifetz, A., Storer, R., McMurray, G., James, T., Morao, I., Aldeghi, M., Bodkin, M., Biggin, P. (2016) Application of an Integrated GPCR SAR-Modelling Platform to Explain the Activation Selectivity of Human 5-HT2C over 5-HT2B, ACS Chemical Biology, 11(5):1372-82. DOI: 10.1021/acschembio.5b01045

Hutchinson, L. G., Gaffney, E. A., Maini, P. K., Wagg, J., Phipps, A., Byrne, H. M. (2016) Vascular Phenotype Identification and Anti-Angiogenic Treatment Recommendation: A Pseudo-Multiscale Mathematical Model of Angiogenesis, Journal of Theoretical Biology, 398: 162-180. DOI: 10.1016/j.jtbi.2016.03.002

Hutton-Smith, L. A., Gaffney, E. A., Byrne, H. M., Maini, P. K., Schwab, D., Mazer, N. A. (2016) A Mechanistic Model of the Intravitreal Pharmacokinetics of Large Molecules and the Pharmacodynamic Suppression of Ocular VEGF Levels by Ranibizumab in Patients with Neovascular Age-Related Macular Degeneration, Molecular Pharmaceutics, Vol. 13, 9, p. 2931-2950. DOI: 10.1021/acs.molpharmaceut.5b00849

Johnstone, R. H., Bardenet, R., Gavaghan, D. J., Mirams, G. R. (2016) Hierarchical Bayesian Inference for Ion Channel Screening Dose-Response Data, Wellcome Open Research, 1:6, DOI:  10.12688/wellcomeopenres.9945.2

Johnstone, R. H., Chang, E., Bardenet, R., de Boer, T., Gavaghan, D., Pathmanathan, P., Clayton, R., Mirams, G. (2015) Uncertainty and Variability in Models of the Cardiac Action Potential: Can We Build Trustworthy Models?, Journal of Molecular and Cellular Cardiology, Volume 96, July 2016, Pages 49-62. DOI: 10.1016/j.yjmcc.2015.11.018

Law, E. C., Wilman, H. R., Kelm, S., Shi, J., Deane, C. M. (2016) Examining the Conservation of Kinks in Alpha Helices, PLoS ONE, 11(6): e0157553. DOI:

Leem, J., Dunbar, J., Georges, G., Shi, J., Deane, C. M. (2016) ABodyBuilder: Automated Antibody Structure Prediction with Data-Driven Accuracy Estimation, MAbs, 8:1-10. DOI: 10.1080/19420862.2016.1205773

Lewin, T., Kim, J., Latifi, K., Poleszczuk, J., Bull, J., Byrne, H., Torres-Roca, J., Moros, E., Gatenby, R., Harrison, L., Heukelom, J., Mohamed, A., Rosenthal, D., Fuller, C., Caudell, J., Enderling, H. (2016) Proliferation Saturation Index Predicts Oropharyngeal Squamous Cell Cancer Gross Tumor Volume Reduction to Prospectively Identify Patients for Adaptive Radiation Therapy, International Journal of Radiation Oncology Biology Physics, 94, 903. DOI: 10.1016/j.ijrobp.2015.12.116

Makola, M. M., Steenkamp, P. A., Dubery, I. A., Kabanda, M. M., Madala, N. E., (2016) Preferential Alkali Metal Adduct Formation by Cis Geometrical Isomers of Dicaffeoylquinic Acids Allows for Efficient Discrimination from their Trans Isomers During Ultra‐High‐Performance Liquid Chromatography/Quadrupole Time‐Of‐Flight Mass Spectrometry, Rapid Communications in Mass Spectrometry, 2016, 30: 1011-1018, DOI: 10.1002/rcm.7526

Mazer, N. A., Schwab, D., Hutton-Smith, L. A., Byrne, H. M., Gaffney, E. A., Maini, P. K., Hartmann, G., Moelleken, J., Gassner, C., Regula, J. T. (2016) What is the biologically relevant KD for VEGF binding to ranibizumab in the eye? A comparison of in-vivo and in-vitro estimates, Conference Publication, ARVO Annual Meeting Abstract, Vol. 57, No. 12.

Nowak, J., Baker, T., Georges, G., Kelm, S., Klostermann, S., Shi, J., Sridharan, S., Deane, C. M. (2016) Length-Independent Structural Similarities Enrich the Antibody CDR Canonical Class Model, MAbs, 8(4):751-60. DOI: 10.1080/19420862.2016.1158370



Atwell, K., Qin, Z., Gavaghan, D., Kugler, H., Hubbard, E., Osborne, J. (2015) Mechano-Logical Model of C. Elegans Germ Line Suggests Feedback on the Cell Cycle, Development, 142(22):3902-11. DOI: 10.1242/dev.126359

Fedorov, O., Castex, J., Tallant, C., Owen, D., Martin, S., Aldeghi, M., Monteiro, O., Filippakopoulos, P., Picaud, S., Trzupek, J., Gerstenberger, B., Bountra, C., Willmann, D., Wells, C., Philpott, M., Rogers, C., Biggin, P., Brennan, P., Bunnage, M., Schule, R., Gunther, T., Knapp, S., Muller, S. (2015) Selective Targeting of the BRG/PB1 Bromodomains Impairs Embryonic and Trophoblast Stem Cell Maintenance, Science Advances, 1(10): e1500723. DOI: 10.1126/sciadv.1500723

Froese, D., Kopec, J., Fitzpatrick, F., Schuller, M., McCorvie, T. J., Chalk, R., Plessl, T., Fettelschoss, V., Fowler, B., Baumgartner, M. R., Yue, W. W. (2015) Structural Insights into the MMACHC-MMADHC Protein Complex Involved in Vitamin B12 Trafficking, Journal of Biological Chemistry, 290(49): 29167-77. DOI: 10.1074/jbc.M115.683268

Khotavivattana, T., Verhoog, S., Tredwell, M., Pfeifer, L., Calderwood, S., Wheelhouse, K., Lee Collier, T., Gouverneur, V. (2015) 18F-Labeling of Aryl-SCF3, -OCF3 and -OCHF2 with [18F] Fluoride, Angewandte Chemie International Edition, 54: 9991–9995. DOI: 10.1002/anie.201504665

Langley, G. W., Brinkø, A., Münzel, M., Walport, L. J., Schofield, C. J., Hopkinson, R. J. (2015) Analysis of JmjC Demethylase-Catalyzed Demethylation Using Geometrically-Constrained Lysine Analogues, ACS Chemical Biology, 11(3):755-62. DOI: 10.1021/acschembio.5b00738

Nazarov, I. B., Schofield, C. J., Terrar, D. A. (2015) Contributions of Cardiac "Funny" (F) Channels and Sarcoplasmic Reticulum Ca2+ In Regulating Beating Rate of Mouse and Guinea Pig Sinoatrial Node, Physiological Reports, 3(12): e12561, DOI: 10.14814/phy2.12561

Taylor-King, J. P., van Loon, E. E., Rosser, G. et Chapman, S. J. (2015) From Birds to Bacteria: Generalised Velocity Jump Processes with Resting States, Bulletin of Mathematical Biology, 77: 1213. DOI:

Verhoog, S., Pfeifer, L., Khotavivattana, T., Calderwood, S., Collier, T., Wheelhouse, K., Tredwell, M., Gouverneur, V. (2015) Silver-Mediated 18F-Labeling of Aryl-CF3 and Aryl-CHF2 with 18F-Fluoride, Synlett, 27(01): 25-28. DOI: 10.1055/s-0035-1560592



Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi J. and Deane, C. M. (2014) SAbDab: the Structural Antibody Database, Nucleic Acids Research, 42, D1140-D1146. DOI: 10.1093/nar/gkt1043

Dunbar, J., Knapp, B. and Deane, C. M. (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study, PLOS Computational Biology, 10(8), e1003748. DOI:

Dunbar, J., Knapp, B., Fuchs, A., Shi J. and Deane, C. M. (2014) Examining Variable Domain Orientations In Antigen Receptors Gives Insight Into TCR-Like Antibody Design, PLOS Computational Biology, 10(9), e1003852. DOI:

Jennings, L. E., Measures, A. R., Wilson, B. G., Conway, S. J. (2014) Phenotypic Screening and Fragment-Based Approaches to the Discovery of Small-Molecule Bromodomain Ligands, Future Medicinal Chemistry, 6, 179–204. DOI: 10.4155/fmc.13.197

Jiao, J., Searle, G.E., Tziortzi, A.C., Salinas, C.A., Gunn, R.N., Schnabel, J.A. (2014) Spatio-Temporal Pharmacokinetic Model Based Registration of 4D Brain PET Neuroimaging Data, Neuroimage, 84:225-35. DOI: 10.1016/j.neuroimage.2013.08.031

Patel, H. J., Blackley, C. L., Cornish, S. L., Hutson, J. M. (2014) Feshbach resonances, molecular bound states and prospects of ultracold molecule formation in mixtures of ultracold K and Cs, Physical Review A 90, 032716/1-10. DOI:

Schiller, R., Scozzafava, G., Tumber, A., Wickens, J. R., Bush, J. T., Rai, G., Lejeune, C., Choi, H., Yeh, T.-L., Chan, M. C., Mott, B. T., McCullagh, J. S. O., Maloney, D. J., Schofield, C. J., Kawamura, A. (2014) A Cell-Permeable Ester Derivative of the Jmjc Histone Demethylase Inhibitor IOX1, ChemMedChem, 9, 566–71. DOI: 10.1002/cmdc.201300428

Wilman, H. R., Shi, J. and Deane, C. M. (2014), Helix Kinks are Equally Prevalent in Soluble and Membrane Proteins, Proteins: Structure, Function, and Bioinformatics, 82: 1960–1970. DOI: 10.1002/prot.24550

Wilman, H. R., Ebejer, J.P., Shi, J., Deane, C. M., Knapp, B. (2014), Crowdsourcing Yields a New Standard for Kinks in Protein Helices, Journal of Chemical Information and Modeling, 54 (9): 2585-2593. DOI: 10.1021/ci500403a



Beattie, K. A., Luscombe, C., Williams, G., Munoz-Muriedas, J., Gavaghan, D.J., Cui, Y., Mirams, G. R. (2013) Evaluation of an In Silico Cardiac Safety Assay: Using Ion Channel Screening Data to Predict QT Interval Changes in the Rabbit Ventricular Wedge, Journal of Pharmacological and Toxicological Methods, 68(1), 88-96. DOI:

Cazares-Körner, C., Pires, I. M., Swallow, I. D., Grayer, S. C., O'Connor, L. J., Olcina, M. M., Christlieb, M., Conway, S.J., Hammond, E. M. (2013) CH-01 is a Hypoxia-Activated Prodrug That Sensitizes Cells to Hypoxia/Reoxygenation Through Inhibition of Chk1 and Aurora A, ACS Chemical Biology, 8(7):1451-9. DOI: 10.1021/cb4001537

Dunbar, J., Fuchs, A., Shi, J., Deane, D. M., Bangle, A. (2013) Characterising The VH-VL Orientation in Antibodies, Protein Engineering, Design & Selection, 26(10), 611-620. DOI: 10.1093/protein/gzt020

Helie, J., Milletti, F., Lelimousin, M., Deane, C., Sansom, M., (2013) Interactions of Two Amphipathic Cell-Penetrating Peptides with Complex Model Membranes: Insights From Molecular Dynamics Simulations, Biophysical Journal, Volume 104 , Issue 2 , 600a. DOI:

Jiao, J., Schnabel, J.A., Gunn, R.N. (2013) A Generalised Spatio-Temporal Registration Framework for Dynamic PET Data: Application to Neuroreceptor Imaging Medical Image Computing and Computer-Assisted Intervention, MICCAI 2013: 16th International Conference, Proceedings, Part I,pp.211-8. DOI 10.1007/978-3-642-40811-3_27

Jiao, J., Searle, G.E., Schnabel, J.A., G.E., Gunn, R.N. (2013) Pharmacokinetic Model Based Groupwise Image Registration of 4D Brain PET Data and its Impact on Clinical Occupancy Studies with [11C]-(+)-PHNO, International Symposium on Cerebral Blood Flow, Metabolism and Function.

Le Page, L. M., Ball, D. R., Ball, V., Mansor, L. S., Heather, L. C., Tyler, D. J. (2013) Assessment of Real-Time Cardiac and Hepatic Glucose Metabolism in the Diabetic Rat Using Hyperpolarised C-13 Pyruvate, Conference Paper, Vol. 30, 42-42.

Lori, C., Lantella, A., Pasquo, A., Alexander, L. T., Knapp, S., Chiaraluce, R. and Consalvi, V. (2013) Effect of Single Amino Acid Substitution Observed in Cancer on Pim-1 Kinase Thermodynamic Stability and Structure, PLOS ONE, 8(6): e64824. DOI:

McKeever, S., Gill, M., Connor, A. J., Johnson, D. (2013) Abstraction in Physiological Modelling Languages (pp. 1–8), Presented at the 3rd International Workshop on Model-driven Approaches for Simulation Engineering.

Mizuta, S., Engle, K. M., Verhoog, S., Galicia-López, O., O’Duill, M., Médebielle, M., Wheelhouse, K., Rassias, G., Thompson, A. L., Gouverneur, V. (2013) Trifluoromethylation of Allylsilanes under Photoredox Catalysis, Organic Letters, 15, 1250-1253. DOI: 10.1021/ol400184t

Mizuta, S., Verhoog, S., Engle, K. M., Khotavivattana, T., O’Duill, M., Wheelhouse, K., Rassias, G., Médebielle, M., Gouverneur, V. (2013) Catalytic Hydrotrifluoromethylation of Unactivated Alkenes, Journal of the American Chemical Society, 135, 2505-2508. DOI: 10.1021/ja401022x

Mizuta, S., Verhoog, S., Wang, X., Shibata, N., Gouverneur, V., Madebielle, M. (2013) Redox chemistry of trifluoromethyl sulfonium salts as CF3 radical sources, Journal of Fluorine Chemistry, Journal of Fluorine Chemistry, 155, 124-131. DOI: 10.1016/j.jfluchem.2013.07.006



Bavro, V. N., De Zorzi, R., Schmidt, M. R., Muniz, J.R., Zubcevic, L., Sansom, M. S., Vénien-Bryan, C., Tucker, S. J. (2012) Structure of a KirBac Potassium Channel with an Open Bundle-Crossing Indicates a Mechanism of Channel Gating, Nature Structural and Molecular Biology, 19(2):158-63. DOI: 10.1038/nsmb.2208.

Connor, A., Cooper, J., Byrne, H., Maini, P., McKeever, S. (2012) Object-Oriented Paradigms for Modelling Vascular Tumour Growth: A Case Study, Proceedings of SIMUL 2012, The Fourth International Conference on Advances in System Simulation, 18.

Dodd, M. S., Ball, D. R., Schroeder, M. A., Le Page, L. M., Atherton, H. J., Heather, L. C., Seymour, A-M., Ashrafian, H., Watkins, H., Clarke, K. and Tyler, D. J. (2012) In Vivo Alterations in Cardiac Metabolism and Function in the Spontaneously Hypertensive Rat Heart, Cardiovascular Research, Volume 95, Issue 1, 1 July 2012, Pages 69–76. DOI:

Gao, Z., Lim, Y. H., Tredwell, M., Li, L., Verhoog, S., Hopkinson, M., Kaluza, W., Collier, T. L., Passchier, J., Huiban, M. and Gouverneur, V. (2012) Metal-Free Oxidative Fluorination of Phenols with [18F]Fluoride, Angewandte Chemie International Edition, 51: 6733–6737. DOI: 10.1002/anie.201201502

Hewings, D. S., Rooney, T. P. C., Jennings, L. E., Hay, D., Schofield, C. J., Brennan, P. E., Knapp, S. and Conway, S. J. (2012) Progress in the Development and Application of Small Molecule Inhibitors of Bromodomain-Acetyl-Lysine Interactions, Journal of Medicinal Chemistry, 55:9393.  DOI: 10.1021/jm300915b

Jiao, J., Salinas, C.A., Searle, G.E., Gunn, R.N., Schnabel, J.A. (2012) Joint Estimation of Subject Motion and Tracer Kinetic Parameters of Dynamic PET Data in an EM Framework, Proceedings, Volume 8314, Medical Imaging: Image Processing; 83140A. DOI: 10.1117/12.911497

Johnson, D., Connor, A. J., McKeever, S. (2012) Modular Markup for Simulating Vascular Tumour Growth, Proceedings of the 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (5th IARWISOCI) - The TUMOR Workshop

Johnson, A., Dunkley, N. C., Mayaud, L., Tsanas, A., Kramer, A., Clifford, G. (2012) Patient-specific Predictions in the Intensive Care Unit using a Bayesian Ensemble, Computing in Cardiology Challenge.

Mizuta, S., Galicia-López, O., Engle, K. M., Verhoog, S., Wheelhouse, K., Rassias, G. and Gouverneur, V. (2012) Trifluoromethylation of Allylsilanes under Copper Catalysis, Chemistry – A European Journal, 18: 8583–8587. doi:10.1002/chem.201201707

Rapedius, M., Schmidt, M. R., Sharma, C., Stansfeld, P. J., Sansom, M. S. P., Baukrowitz, T., Tucker, S. J (2012) State-Independent Intracellular Access of Quaternary Ammonium Blockers to the Pore of TREK-1, Channels (Austin), Nov-Dec, 6(6):473-8. DOI: 10.4161/chan.22153

Ross, G. A., Morris, G. M., Biggin, P. C. (2012) Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites, PLoS ONE, 7(3): e32036. DOI:

Schmidt, M.R., Stansfeld, P. J., Tucker, J. S. and Sansom, M. S. P. (2012) Simulation-Based Prediction of Phosphatidylinositol 4,5-Bisphosphate Binding to an Ion Channel, Biochemistry, 52 (2), 279-281. DOI: 10.1021/bi301350s