Publications

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, IN PRESS, [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

Sebastian Kelm, Yoonjoo Choi and Charlotte M. Deane
Protein Modelling and Structural Prediction
Springer Handbook of Bio- and Neuroinformatics
(in press)

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).