University of Oxford Logo

Research Interests
Group Members


132. Matthew Raybould, Claire Marks, Konrad Krawczyk, Bruck Taddese, Jaroslaw Nowak, Alan P Lewis, Alexander Bujotzek, Jiye Shi, Charlotte M Deane, Five computational developability guidelines for therapeutic antibody profiling, PNAS, 2019, , [Paper Link]

131. Claire Marks, Charlotte M. Deane, Increasing the accuracy of protein loop structure prediction with evolutionary constraints, Bioinformatics, 2018, bty996, [Paper Link]

130. Bernhard Knapp, Luis Ospina, Charlotte M. Deane, Avoiding false positive conclusions in molecular simulation: the importance of replicas, Journal of Chemical Theory and Computation, 2018, , [Paper Link]

129. Wing Ki Wong, Guy Georges, Francesca Ros, Sebastian Kelm, Alan P Lewis, Bruck Taddese, Jinwoo Leem, Charlotte M Deane, SCALOP: sequence-based antibody canonical loop structure annotation, Bioinformatics, 2018, , bty877 [Paper Link]

128. Fergus Imrie, Anthony Bradley, Mihaela van der Schaar, Charlotte M Deane, Protein Family-specific Models using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data, Journal of Chemical Information and Modeling, 2018, , [Paper Link]

127. Aleksandr Kovaltsuk, Konrad Krawczyk, Sebastian Kelm, James Snowden, Charlotte M Deane, Filtering Ig-seq data using antibody structural information, The Journal of Immunology, 2018, , [No Link Available]

126. Luis Ospina-Foreroi, Charlotte M Deane, Gesine Reinert, Assessment of model fit via network comparison methods based on subgraph counts, Journal of Complex Networks, 2018, cny017, [Paper Link]

125. Konrad Krawczyk, Sebastian Kelm, Aleksandr Kovaltsuk, Jacob D. Galson, Dominic Kelly, Johannes Trück, Cristian Regep, Jinwoo Leem, Wing K. Wong, Jaroslaw Nowak, James Snowden, Michael Wright, Laura Starkie, Anthony Scott-Tucker, Jiye Shi, Charlotte M. Deane, Structurally Mapping Antibody Repertoires, Front. Immunol., 2018, , [Paper Link]

124. Matthew Raybould, Claire Marks, Konrad Krawczyk, Bruck Taddese, Jaroslaw Nowak, Alan P Lewis, Alexander Bujotzek, Jiye Shi, Charlotte M Deane, The Therapeutic Antibody Profiler (TAP): Five Computational Developability Guidelines, bioRxiv, 2018, , [Paper Link]

123. Aleksandr Kovaltsuk, Jinwoo Leem, Sebastian Kelm, James Snowden, Charlotte M Deane, Konrad Krawczyk, Observed Antibody Space: a resource for data mining next generation sequencing antibody repertoires, The Journal of Immunology, 2018, 201(8), 2502-2509 [No Link Available]

122. Saulo H. P. de Oliveira, Charlotte M. Deane, Combining co-evolution and secondary structure prediction to improve fragment library generation, Bioinformatics, 2018, 34, 2219-2227 [Paper Link]

121. Kanti V Mardia, Karthik Sriram, and Charlotte M Deane, A statistical model for helices with applications, Biometrics, 2018, , 10.1111/biom.12870 [Paper Link]

120. Jinwoo Leem, Guy Georges, Jiye Shi, Charlotte M. Deane, Antibody side chain conformations are position-dependent, Proteins, 2018, 10.1002/prot.25453, [Paper Link]

119. Anatol E. Wegner, Luis Ospina-Forero, Robert E. Gaunt, Charlotte M. Deane, Gesine Reinert, Identifying networks with common organizational principles, Journal of Complex Networks, 2017, , cny003 [Paper Link]

118. Bernhard Knapp, Marta Alcala, Hao Zhang, Clare West, P. Anton van der Merwe, Charlotte M. Deane, pyHVis3D: Visualising Molecular Simulation deduced H-bond networks in 3D: Application to T-cell receptor interactions, Bioinformatics, 2017, btx842, [Paper Link]

117. Aleksandr Kovaltsuk, Konrad Krawczyk, Jacob D. Galson, Dominic F. Kelly, Charlotte M. Deane, Johannes Truck, How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data, Front. Immunol, 2017, 8, 1753 [Paper Link]

116. Claire Marks, Jiye Shi, Charlotte M. Deane, Predicting Loop conformational ensembles, Bioinformatics, 2017, btx718, [Paper Link]

115. Saulo H. P. de Oliveira, Eleanor C. Law, Jiye Shi, Charlotte M. Deane, Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction, Bioinformatics, 2017, btx722, [Paper Link]

114. MD Lecken, MJT Page, AJ Crosby, S Mason, G Reinert, CM Deane, CommWalker: Correctly Evaluating Modules in Molecular Networks in Light of Annotation Bias, Bioinformatics, 2017, , btx706 [Paper Link]

113. Jinwoo Leem, Saulo de Oliveira, Konrad Krawczyk, Charlotte M. Deane, STCRDab: the structural T-cell receptor database, NAR, 2017, gkx971, [Paper Link]

112. Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M. Deane, Peter Minary, In silico structural modeling of multiple epigenetic marks on DNA, Bioinformatics, 2017, btx516, [Paper Link]

111. Saulo de Oliveira, Charlotte M Deane, Co-evolution techniques are reshaping the way we do structural bioinformatics, F1000Research, 2017, 6, 1224 [Paper Link]

110. Bernhard Knapp, James Dunbar, Marta Alcala, Charlotte M Deane, Variable Regions of Antibodies and T-cell Receptors may not be Sufficient in Molecular Simulations Investigating Binding, Journal of Chemical Theory and Computation, 2017, 13(7), i3097-3105 [Paper Link]

109. Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J Gavaghan, Charlotte M Deane, Bernhard Knapp, 10 simple rules for surviving an interdisciplinary PhD, PLOS Comp Bio, 2017, 13(5), e1005512 [Paper Link]

108. Cristian Regep, Guy Georges, Jiye Shi, Bojana Popovic, Charlotte M Deane, The H3 loop of antibodies shows unique structural characteristics, Proteins, 2017, , 10.1002/prot.25291 [Paper Link]

107. Jack WC Chen, Zhuo A Chen, Kacper Rogala, Jeremy Metz, Charlotte M Deane, Juri Rappsilber, and James G Wakefield, Cross-linking mass spectrometry identifies new interfaces of Augmin required to localise the γ-Tubulin Ring Complex to the mitotic spindle, Biology Open, 2017, 6(5), 654-663 [Paper Link]

106. Nicholas Pearce, Tobias Krojer, Anthony Bradley, Patrick Collins, Radosław Nowak, Romain Talon, Brian Marsden, Sebastian Kelm, Jiye Shi, Charlotte M. Deane, and Frank von Delft, A Multi-Crystal Method for Extracting Obscured Crystallographic States from Conventionally Uninterpretable Electron Density, Nature Communications, 2017, 8, 15123 [Paper Link]

105. Claire Marks, Charlotte M Deane, Antibody H3 Structure Prediction, Computational and Structural Biotechnology, 2017, 1(15), 222-231 [Paper Link]

104. Tom Parks, Mariana M. Mirabel, Joseph Kado, Kathryn Auckland, Jaroslaw Nowak, Anna Rautanen, Alexander Mentzer, Eloi Marijon, Xavier Jouven, Mai Ling Perman, Tuliana Cua, John K. Kauwei, John B. Allen, Henry Taylor, Kathryn J. Robson, Charlotte M. Deane, Andrew C. Steer, Adrian V. S. Hill, Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania, Nature Communications, 2017, 8, 14946 [Paper Link]

103. Nicholas M Pearce, Anthony R Bradley, Brian D Marsden, Charlotte M Deane, Frank von Delft, Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites, Structural Dynamics, 2017, 4(3), 032104 [Paper Link]

102. Charlotte M Deane, Maximiliano Vasquez, Developability of Biotherapeutics: Computational Approaches. Edited by Sandeep Kumar and Satish K. Singh, MAbs, 2017, 9, 1,2017 [Paper Link]

101. Claire Marks, Jaroslaw Nowak, Stefan Klostermann, Guy Georges, James Dunbar, Jiye Shi, Sebastian Kelm, Charlotte M Deane, Sphinx:Merging knowledge-based and ab initio approaches to improve protein loop prediction, Bioinformatics, 2017, 33((9), 1346-1353 [Paper Link]

100. Konrad Krawczyk, James Dunbar, Charlotte M Deane, Computational Tools for Aiding Rational Antibody Design, Methods Mol Biol, 2017, 1529, 399-416 [Paper Link]

99. Hao Zhang, Hong-Sheng Lim, Berhard Knapp, Charlotte M. Deane, Milos Aleksic, Omer Dushek, P. Anton van der Merwe, The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding, Scientific Reports, 2016, 6, 35326 [Paper Link]

98. Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M Deane, Comparing co-evolution methods and their application to template-free protein structure prediction, Bioinformatics, 2017, 33(3), 373-381 [Paper Link]

97. Konrad Krawczyk, Adelene Sim, Bernhard Knapp, Charlotte M. Deane, Peter Minary, Tertiary element interaction in HIV-1 TAR, Journal of Chemical Information and Modeling, 2016, 56(9), 1746-1754 [Paper Link]

96. Charlotte M. Deane, Ian D. Wall, Darren V.S. Green, Brian D. Marsden and Anthony R. Bradley, WONKA and OOMMPPAA - analysis of protein-ligand interaction data to direct Structure Based Drug Design, Acta Crystallographica Section D, 2017, 73(3), 279-285 [Paper Link]

95. Sam Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary, Modelling Functional Motions of Biological Systems by Customised Natural Moves, Biophysical Journal, 2016, 111(4), 710-721 [Paper Link]

94. Jinwoo Leem, James Dunbar, Guy Georges, Jiye Shi, Charlotte M Deane, ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation, mAbs, 2016, 8(7), 1259-1268 [Paper Link]

93. Waqar Ali, Anatol E Wegner, Robert E. Gaunt, Charlotte M Deane, and Gesine Reinert, Comparison of large networks with sub-sampling strategies, Scientific Reports, 2016, 6, 28955 [Paper Link]

92. Eleanor C Law, Henry R Wilman, Sebastian Kelm, Jiye Shi, Charlotte M Deane, Examining the conservation of kinks in alpha helices, PLOS ONE, 2016, 11(6), e0157553 [Paper Link]

91. James Dunbar, Konrad Krawczyk, Jinwoo Leem, Claire Marks, Jaroslaw Nowak, Cristian Regep, Guy Georges, Sebastian Kelm, Bojana Popovic, Charlotte M Deane, SAbPred: a structure-based antibody prediction server, Nucleic Acids Research, 2016, 44(W1), W474-W487 [Paper Link]

90. Jaroslaw Nowak, Terry Baker, Guy Georges, Sebastian Kelm, Stefan Klostermann, Jiye Shi, Sudharsan Sridharan, Charlotte M Deane, Length-independent structural similarities enrich the antibody CDR canonical class model, mAbs, 2016, 8(4), 751-760 [Paper Link]

89. Bernhard Knapp, Charlotte M Deane, T-cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex, J. Chem. Inf. Model, 2015, 56(1), 46-53 [Paper Link]

88. James Dunbar, Charlotte M Deane, ANARCI: Antigen receptor numbering and receptor classification, Bioinformatics, 2015, 32(2), 298-300 [Paper Link]

87. A R Bradley, I D Wall, Frank von Delft, D V S Green, C M Deane, B D Marsden, WONKA - Objective Novel Complex Analysis for ensembles of protein-ligand structures, Journal of Computer-Aided Molecular Design, 2015, 29(10), 963-73 [Paper Link]

86. Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, and Peter Minary, Exploring peptide/MHC detachment processes using Hierarchical Natural Move Monte Carlo, Bioinformatics, 2015, 32(2), 181-186 [Paper Link]

85. Hannah Edwards, Charlotte M Deane, Structural bridges through fold space, Plos Comp Biol., 2015, 11(9), e1004466 [Paper Link]

84. Leila T. Alexander, Henrik Mobitz, Peter Drueckes, Pavel Savitsky, Oleg Fedorov, Jonathan M. Elkins, Charlotte M. Deane, Sandra W. Cowan-Jacob, and Stefan Knapp, Type II Inhibitors Targeting CDK2, ACS Chem. Biol., 2015, 10(9), i2116-2125 [Paper Link]

83. Valeria Palumbo, Claudia Pellacani, Kate J Heesom, Kacper B Rogala, Charlotte M Deane, Violaine Mottier-Pavie, Maurizio Gatti, Silvia Bonaccorsi, James G Wakefield, Misato Controls Mitotic Microtubule Generation by Stabilizing the Tubulin Chaperone Protein-1 Complex, Current Biology, 2015, 25(13), 1777-1783 [Paper Link]

82. Shunzhou Wan, Bernhard Knapp, David W. Wright, Charlotte M. Deane, Peter V. Coveney, Rapid, Precise, and Reproducible Prediction of Peptide.MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment, J. Chem. Theory Comput., 2015, 11(7), 3346-3356 [Paper Link]

81. Kacper B Rogala, Nicola J Dynes, Georgios N Hatzopoulos, Jun Yan, Sheng Kai Pong, Carol V Robinson, Charlotte M Deane, Pierre Gonczy, Ioannis Vakonakis, The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation, eLife, 2015, 4, e07410 [Paper Link]

80. Reyhaneh Esmaielbeiki, Koonrad Krawczyk, Bernhard Knapp, Jean-Christophe Nebel, Charlotte M. Deane, Progress and challenges in predicting protein interfaces, Briefings in Bioinformatics, 2015, doi: 10.1093/bib/bbv027, [Paper Link]

79. Saulo Henrique Pires de Oliveira, Jiye Shi, Charlotte M Deane, Building a better fragment library for de novo protein structure prediction, Plos One, 2015, 10(4), e0123998 [Paper Link]

78. Bernhard Knapp, Remi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg McInerny, Timo Minssen, James Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M Deane, Ten simple rules for a successful cross-disciplinary collaboration, Plos Comp. Bio, 2015, 11(4), e1004214 [Paper Link]

77. M. Gerstel, C. M. Deane, E. F. Garman, Identifying and quantifying radiation damage at the atomic level, J. Synchrotron Rad., 2015, 22, doi:10.1107/S1600577515002131 [Paper Link]

76. Bernhard Knapp, Samuel Demharter, Reyhaneh Esmaielbeiki, Charlotte M. Deane, Current Status and Future Challenges in T-cell receptor / peptide / MHC Molecular Dynamics Simulations, Briefings in Bioinformatics, 2015, 10.1093/bib/bbv005, [Paper Link]

75. Alexander Bujotzek, James Dunbar, Florian Lipsmeier, Wolfgang Schafer, Iris Antes, Charlotte M Deane, Guy Georges, Prediction of VH.VL domain orientation for antibody variable domain modeling, Proteins, 2015, 83(4), 681-695 [Paper Link]

74. Anthony R. Bradley, Ian D. wall, Darren V. V. Green, Charlotte M Deane, Brian D Marsden, OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data, Journal of Chemical Information and Modeling, 2014, 54(10), 2636-2646 [Paper Link]

73. James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M Deane, Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design, Plos Comp. Bio, 2014, 10(9), e1003852 [Paper Link]

72. Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M Deane, Bernhard Knapp, Crowdsourcing yields a new standard for kinks in protein helices, Journal of Chemical Information and Modeling, 2014, 54(9), 2585-2593 [Paper Link]

71. Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M Deane, Alignment-free protein interaction network comparison, Bioinformatics, 2014, 30(17), i430-i437 [Paper Link]

70. Bernhard Knapp, James Dunbar, Charlotte M Deane, 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 Comp Bio, 2014, 10(8), e1003748 [Paper Link]

69. Hung Dien, Charlotte M. Deane, Bernhard Knapp, Gro2mat: A package to efficiently read gromacs output in MATLAB, J. Comput. Chem., 2014, 10.1002/jcc.23650, [Paper Link]

68. K Krawczyk, X Liu, T Baker, J Shi, CM Deane, Improving B-cell epitope prediction and its application to global antibody-antigen docking, Bioinformatics, 2014, 30(16), 2288-2294 [Paper Link]

67. James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David J. Gavaghan, Stephen Emmott, Charlotte Deane, Ten Simple Rules for Effective Computational Research, PLOS Computational Biology, 2014, 10(3), 1003506 [Paper Link]

66. H.R. Wilman, J. Shi, C.M. Deane, Helix kinks are equally prevalent in soluble and membrane proteins, Proteins, 2014, 82(9), 1960-70 [Paper Link]

65. H. Edwards, S. Abeln, C.M. Deane, Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies, Plos Computational biology, 2013, 9(11), e1003325 [Paper Link]

64. J. Dunbar, K. Krawzyk, J. Leem, T. Baker, A. Fuchs, G. Georges, J. Shi, C.M. Deane, SAbDab: the Structural Antibody Database, NAR, 2014, 42, D1140-D1146 [Paper Link]

63. Konrad Krawczyk, Terry Baker, Jiye Shi, Charlotte M. Deane, Antibody i-Patch prediction of the antibody binding site improves rigid local antibody antigen docking, PEDS, 2013, 26(10), 621-629 [Paper Link]

62. J. Dunbar, A. Fuchs, J. Shi, CM. Deane, ABangle: Characterising the VH-VL orientation in antibodies, PEDS, 2013, 26(10), 611-620 [Paper Link]

61. Jean-Paul Ebejer, Jamie Hill, Sebastian Kelm, Jiye Shi, Charlotte M. Deane, Memoir: template based structure prediction for membrane proteins, Nucleic Acid Research, 2013, 41(W1), W379-W383 [Paper Link]

60. Sebastian Kelm, Anna Vangone, Yoonjoo Choi, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Fragment-based modelling of membrane protein loops - successes, failures and prospects for the future, Proteins, 2014, 82: 175-186, doi: 10.1002/prot.24299 [Paper Link]

59. Qiang Luo, Rebecca Hamer, Gesine Reinert, Charlotte M Deane, Local Network Patterns in Protein-Protein Interfaces, PLOS ONE, 2013, 8(3), e57031 [Paper Link]

58. Yoonjoo Choi, Sumeet Agarwal, Charlotte M. Deane, How long is a piece of loop?, Peerj, 2013, 1, e1 [Paper Link]

57. Jamie R. Hill, Charlotte M. Deane, MP-T: improving membrane protein alignment for structure prediction, Bioinformatics, 2012, 29(1), 54-61 [Paper Link]

56. Lewis AC, Jones NS, Porter MA, Deane CM, What evidence is There for the Homology of Protein-Protein interactions, PloS Comp. Bio., 2012, 8(9), e1002645 [Paper Link]

55. Mireille Gomes, Rebecca Hamer, Gesine Reinert, and Charlotte M Deane, Mutual information and variants for protein domain-domain contact prediction, BMC Research Notes, 2012, 5, 472 [Paper Link]

54. Rito T, Deane CM, Reinert G., The importance of age and high degree, in protein-protein interaction networks, J Comput Biol., 2012, 19(6), 785-95 [Paper Link]

53. Sonja Pawelczyk, Kathryn A. Scott, Rebecca Hamer, Gareth Blades, Charlotte M. Deane, George H. Wadhams, Predicting Inter-Species Cross-Talk in Two-Component Signalling Systems, PloS ONE, 2012, 7(5), e37737 [Paper Link]

52. Martin Mann, Rhodri Saunders, Cameron Smith, Rolf Backofen, Charlotte M. Deane, Producing high-accuracy lattice models from protein atomic co-ordinates including side chains, Advances in Bioinformatics, 2012, 148045, [Paper Link]

51. Ebejer JP, Morris GM, Deane CM., Freely Available Conformer Generation Methods: How Good Are They?, J Chem Inf Model., 2012, , [Paper Link]

50. Junaid Kashir, Michalis Konstantinidis, Celine Jones, Bernadette Lemmon, Hoi Chang Lee, Rebecca Hamer, Bjorn Heindryckx, Charlotte M. Deane, Petra De Sutter, Rafael A. Fissore, John Parrington, Dagan Wells, and Kevin Coward, A maternally inherited autosomal point mutation in human phospholipase C zeta (PLC.) leads to male infertility, Hum. Reprod., 2012, 27(1), 222-31 [Paper Link]

49. Choi Y, Deane CM, Predicting antibody complementarity determining region structures without classification, Mol. BioSyst., 2011, 7(12), 3327-34 [Paper Link]

48. Saunders R, Deane CM, The imprint of codons on protein structure, Biotechnology Journal, 2011, 6(6), 641-9 [Paper Link]

47. Hill JR, Kelm S, Shi J, Deane CM, Environment specific substitution tables improve membrane protein alignment, Bioinformatics, 2011, 27(13), 15-i23 [Paper Link]

46. Saunders R, Mann M, Deane CM, Signatures of co-translational folding, Biotechnology Journal, 2011, 6(6), 742-51 [Paper Link]

45. Kelm S, Shi J, Deane CM, MEDELLER: Homology-Based Coordinate Generation for Membrane Proteins, Bioinformatics, 2010, 26(22), 2833-40 [Paper Link]

44. Ali W, Deane CM, Evolutionary analysis reveals low coverage as the major challenge for protein interaction network alignment, Molecular Biosystem, 2010, 6(11), 2296-2304 [Paper Link]

43. Rito T, Wang Z, Deane CM, Reinert G, How threshold behaviour affects the use of subgraphs for network comparison, Bioinformatics, 2010, 26, i611-i617 [Paper Link]

42. Lewis AC, Jones NS, Porter MA, Deane CM, The function of communities in protein interaction networks at multiple scales, BMC Syst Biol., 2010, 4(1), 100 [Paper Link]

41. Lance BK, Deane CM, Wood GR, Exploring the potential of template-based modelling, Bioinformatics, 2010, 26(15), 1849-56 [Paper Link]

40. Hamer R, Luo Q, Armitage JP, Reinert G, Deane CM, i-Patch: Interprotein contact prediction using local network information, Proteins, 2010, 78(13), 2781-97 [Paper Link]

39. Saunders R, Deane CM, Synonymous codon usage influences the local protein structure observed, Nucleic Acids Res., 2010, 38(19), 6719-28 [Paper Link]

38. Agarwal S, Deane CM, Porter MA, Jones NS, Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks, PLoS Comput Biol., 2010, 6(6), e1000817 [Paper Link]

37. Ellis JJ, Huard FP, Deane CM, Srivastava S, Wood GR, Directionality in protein fold prediction, BMC Bioinformatics, 2010, 11, 172 [Paper Link]

36. Hamer R, Chen PY, Armitage JP, Reinert G, Deane CM, Deciphering chemotaxis pathways using cross species comparisons, BMC Syst Biol., 2010, 4, 3 [Paper Link]

35. Choi Y, Deane CM, FREAD revisited: Accurate loop structure prediction using a database search algorithm, Proteins, 2010, 78(6), 1431-40 [Paper Link]

34. Saunders R, Deane CM, Protein structure prediction begins well but ends badly, Proteins, 2010, 78(5), 1282-90 [Paper Link]

33. Lewis AC, Saeed R, Deane CM, Predicting protein-protein interactions in the context of protein evolution, Mol Biosyst., 2010, 6(1), 55-64 [Paper Link]

32. Ali W, Deane CM, Functionally guided alignment of protein interaction networks for module detection, Bioinformatics, 2009, 25(23), 3166-73 [Paper Link]

31. Patel PC, Fisher KH, Yang EC, Deane CM, Harrison RE, Proteomic analysis of microtubule-associated proteins during macrophage activation, Mol Cell Proteomics., 2009, 8(11), 2500-14 [Paper Link]

30. Heytens E, Parrington J, Coward K, Young C, Lambrecht S, Yoon SY, Fissore RA, Hamer R, Deane CM, Ruas M, Grasa P, Soleimani R, Cuvelier CA, Gerris J, Dhont M, Deforce D, Leybaert L, De Sutter P, Reduced amounts and abnormal forms of phospholipase C zeta (PLCzeta) in spermatozoa from infertile men, Hum Reprod., 2009, 24(10), 2417-28 [Paper Link]

29. Kelm S, Shi J, Deane CM, iMembrane: homology-based membrane-insertion of proteins, Bioinformatics, 2009, 25(8), 1086-8 [Paper Link]

28. Fisher KH, Deane CM, Wakefield JG, The functional domain grouping of microtubule associated proteins, Commun Integr Biol., 2008, 1(1), 47-50 [Paper Link]

27. Chen PY, Deane CM, Reinert G, Predicting and validating protein interactions using network structure, PLoS Comput Biol., 2008, 4(7), e1000118 [Paper Link]

26. Valeyev NV, Downing AK, Sondek J, Deane C, Electrostatic and functional analysis of the seven-bladed WD beta-propellers, Evol Bioinform Online, 2008, 4, 203-16 [Paper Link]

25. Hughes JR, Meireles AM, Fisher KH, Garcia A, Antrobus PR, Wainman A, Zitzmann N, Deane C, Ohkura H, Wakefield JG, A microtubule interactome: complexes with roles in cell cycle and mitosis, PLoS Biol., 2008, 6(4), e98 [Paper Link]

24. Saeed R, Deane C, An assessment of the uses of homologous interactions, Bioinformatics, 2008, 24(5), 689-95 [Paper Link]

23. Deane CM, Dong M, Huard FP, Lance BK, Wood GR, Cotranslational protein folding--fact or fiction?, Bioinformatics, 2007, 23(13), i142-8 [Paper Link]

22. Chen PY, Deane CM, Reinert G, A statistical approach using network structure in the prediction of protein characteristics, Bioinformatics, 2007, 23(17), 2314-21 [Paper Link]

21. Abeln S, Teubner C, Deane CM, Using phylogeny to improve genome-wide distant homology recognition, PLoS Comput Biol., 2007, 3(1), e3 [Paper Link]

20. Abeln S, Deane CM, Linking evolution of protein structures through fragments, BMC Systems Biology, 2007, 1(Suppl 1), S12 [No Link Available]

19. Huard FP, Deane CM, Wood GR, Modelling sequential protein folding under kinetic control, Bioinformatics, 2006, 22(14), e203-10 [Paper Link]

18. Saeed R, Deane CM, Protein protein interactions, evolutionary rate, abundance and age, BMC Bioinformatics, 2006, 7, 128 [Paper Link]

17. Winstanley HF, Abeln S, Deane CM, How old is your fold?, Bioinformatics, 2005, Suppl 1, i449-58 [Paper Link]

16. Abeln S, Deane CM, Fold usage on genomes and protein fold evolution, Proteins, 2005, 60(4), 690-700 [Paper Link]

15. O'Leary JM, Hamilton JM, Deane CM, Valeyev NV, Sandell LJ, Downing AK, Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA, J Biol Chem., 2004, 279(51), 53857-66 [Paper Link]

14. Deane CM, Salwinski L, Xenarios I, Eisenberg D, Protein interactions: two methods for assessment of the reliability of high throughput observations, Mol Cell Proteomics, 2002, 1(5), 349-56 [Paper Link]

13. Williams MG, Shirai H, Shi J, Nagendra HG, Mueller J, Mizuguchi K, Miguel RN, Lovell SC, Innis CA, Deane CM, Chen L, Campillo N, Burke DF, Blundell TL, de Bakker PI, Sequence-structure homology recognition by iterative alignment refinement and comparative modeling, Proteins, 2001, Suppl 5, 92-7 [Paper Link]

12. Deane CM, Kaas Q, Blundell TL, SCORE: predicting the core of protein models, Bioinformatics, 2001, 17(6), 541-50. [Paper Link]

11. Deane CM, Lummis SC, The role and predicted propensity of conserved proline residues in the 5-HT3 receptor, J Biol Chem, 2001, 276(41), 37962-6 [Paper Link]

10. Burke DF, Deane CM, Improved loop prediction from sequence alone, Protein Eng., 2001, 14(7), 473-8 [Paper Link]

9. Deane CM, Blundell TL, CODA: a combined algorithm for predicting the structurally variable regions of protein models, Protein Sci., 2001, 10(3), 599-612 [Paper Link]

8. Burke DF, Deane CM, Blundell TL, Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure, Bioinformatics, 2000, 16(6), 513-9 [Paper Link]

7. Deane CM, Blundell TL, A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins, Proteins, 2000, 40(1), 135-44 [Paper Link]

6. Deane CM, Allen FH, Taylor R, Blundell TL, Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid, Protein Eng., 1999, 12(12), 1025-8 [Paper Link]

5. Burke DF, Deane CM, Nagarajaram HA, Campillo N, Martin-Martinez M, Mendes J, Molina F, Perry J, Reddy BV, Soares CM, Steward RE, Williams M, Carrondo MA, Blundell TL, Mizuguchi K, An iterative structure-assisted approach to sequence alignment and comparative modeling, Proteins, 1999, Suppl 3, 55-60 [Paper Link]

4. Mizuguchi K, Deane CM, Blundell TL, Overington JP, HOMSTRAD: a database of protein structure alignments for homologous families, Protein Sci., 1998, 7(11), 2469-71 [Paper Link]

3. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP, JOY: protein sequence-structure representation and analysis, Bioinformatics, 1998, 14(7), 617-23 [Paper Link]

2. Sowdhamini R, Burke DF, Deane C, Huang JF, Mizuguchi K, Nagarajaram HA, Overington JP, Srinivasan N, Steward RE, Blundell TL, Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies, Acta Crystallogr D Biol Crystallogr., 1998, 54(Pt 6 Pt 1), 1168-77 [Paper Link]

1. Deane CM, Kroemer RT, Richards WG, A structural model of the human thrombopoietin receptor complex, J Mol Graph Model, 1997, 15(3), 170-8, 185-8 [Paper Link]

Book Chapters

Jinwoo Leem and Charlotte M. Deane
High-Throughput Antibody Structure Modeling and Design Using ABodyBuilder
Computational Methods in Protein Evolution
DOI 978-1-4939-8736-8_21, © 2019

Konrad Krawczyk, James Dunbar, and Charlotte M. Deane
Computational Tools for Aiding Rational Antibody Design
Computational Protein Design
DOI 978-1-4939-6637-0_21, © 2017

Sebastian Kelm, Yoonjoo Choi and Charlotte M. Deane
Protein Modelling and Structural Prediction
Springer Handbook of Bio- and Neuroinformatics
DOI 978-3-642-30574-0_11, © 2014

Waqar Ali, Charlotte M. Deane and Gesine Reinert
Protein interaction networks and their statistical analysis in Handbook of Statistical Systems Biology (in press)
eds Michael P. H. Stumpf, David J. Balding and Mark A. Girolami
John Wiley & Sons, 2010

Charlotte M. Deane and Tom L. Blundell
Protein comparative modeling and drug discovery in The practice of medicinal chemistry,
eds CG Wermuth

Charlotte M. Deane and Tom L. Blundell
Examination of the less favoured regions of the Ramachandran plot in Perspectives in structural biology,
eds. Vijayan, M., Yathindra, N.and Kolaskar, A. S. (Indian Academy of Sciences, Hyderabad) (1999).

Oxford Spires
Department of Statistics