Publications

A full list of the group's publications can be found below. Click on the relevant years to see the corresponding papers. You can also download this information as a bibtex file here.

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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, pages btw823
Zhang, H., Lim, H.S., Knapp, B., Deane, C.M., Aleksic, M., Dushek, O. & van der Merwe, P.A. (2016) The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding Sci. Rep., 6:35326
de Oliveira, S.H.P., Shi, J. & Deane, C.M. (2016) Comparing co-evolution methods and their application to template-free protein structure prediction. Bioinformatics, pages btw618
Krawczyk, K., Sim, A.Y.L., Knapp, B., Deane, C.M. & Minary, P. (2016) Tertiary Element Interaction in HIV-1 TAR J. Chem. Inf. Model., 56(9):1746-1754
Deane, C.M., Marsden, B.D., Wall, I.D., Green, D.V.S. & Bradley, A.R. (2016) WONKA and OOMMPPAA – analysis of protein-ligand interaction data to direct Structure Based Drug Design Acta Crystallogr. Sect. D
Demharter, S., Knapp, B., Deane, C.M. & Minary, P. (2016) Modeling Functional Motions of Biological Systems by Customized Natural Moves Biophys. J., 111(4):710-721
Leem, J., Dunbar, J., Georges, G., Shi, J. & Deane, C.M. (2016) ABodyBuilder: automated antibody structure prediction with data–driven accuracy estimation MAbs, 8(7):1259-1268
Ali, W., Wegner, A.E., Gaunt, R.E., Deane, C.M. & Reinert, G. (2016) Comparison of large networks with sub-sampling strategies Sci. Rep., 6:28955
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
Dunbar, J., Krawczyk, K., Leem, J., Marks, C., Nowak, J., Regep, C., Georges, G., Kelm, S., Popovic, B. & Deane, C.M. (2016) SAbPred: a structure-based antibody prediction server. Nucleic Acids Res., 44(W1):W474-W478
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
Knapp, B. & Deane, C.M. (2015) T-cell Receptor Binding Effects the Dynamics of the Peptide/MHC-I Complex. J. Chem. Inf. Model.
Dunbar, J. & Deane, C.M. (2015) ANARCI: Antigen receptor numbering and receptor classification Bioinformatics, pages btv552
Knapp, B., Demharter, S., Esmaielbeiki, R. & Deane, C.M. (2015) Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations Brief. Bioinform.
Esmaielbeiki, R., Krawczyk, K., Knapp, B., Nebel, J.C. & Deane, C.M. (2015) Progress and challenges in predicting protein interfaces Brief. Bioinform.
Knapp, B., Bardenet, R., Bernabeu, M.O., Bordas, R., Bruna, M., Calderhead, B., Cooper, J., Fletcher, A.G., Groen, D., Kuijper, B., Lewis, J., McInerny, G., Minssen, T., Osborne, J., Paulitschke, V., Pitt-Francis, J., Todoric, J., Yates, C.A., Gavaghan, D. & Deane, C.M. (2015) Ten Simple Rules for a Successful Cross-Disciplinary Collaboration. PLoS Comput. Biol., 11(4):e1004214
de Oliveira, S.H.P., Shi, J. & Deane, C.M. (2015) Building a better fragment library for de novo protein structure prediction. PLoS One, 10(4):e0123998
Bradley, A.R., Wall, I.D., von Delft, F., Green, D.V.S., Deane, C.M. & Marsden, B.D. (2015) WONKA: objective novel complex analysis for ensembles of protein-ligand structures. J. Comput. Aided. Mol. Des.
Knapp, B., Demharter, S., Deane, C.M. & Minary, P. (2015) Exploring peptide/MHC detachment processes using Hierarchical Natural Move Monte Carlo Bioinformatics, pages btv502
Edwards, H. & Deane, C.M. (2015) Structural Bridges through Fold Space. PLoS Comput. Biol., 11(9):e1004466
Alexander, L.T., Möbitz, H., Drueckes, P., Savitsky, P., Fedorov, O., Elkins, J.M., Deane, C.M., Cowan-Jacob, S.W. & Knapp, S. (2015) Type II Inhibitors Targeting CDK2. ACS Chem. Biol., 10(9):2116-25
Palumbo, V., Pellacani, C., Heesom, K.J., Rogala, K.B., Deane, C.M., Mottier-Pavie, V., Gatti, M., Bonaccorsi, S. & Wakefield, J.G. (2015) Misato Controls Mitotic Microtubule Generation by Stabilizing the Tubulin Chaperone Protein-1 Complex. Curr. Biol.
Rogala, K.B., Dynes, N.J., Hatzopoulos, G.N., Yan, J., Pong, S.K., Robinson, C.V., Deane, C.M., Gönczy, P. & Vakonakis, I. (2015) The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation Elife, 4:e07410
Bujotzek, A., Dunbar, J., Lipsmeier, F., Schäfer, W., Antes, I., Deane, C.M. & Georges, G. (2015) Prediction of VH-VL domain orientation for antibody variable domain modeling. Proteins, 83(4):681-95
Gerstel, M., Deane, C.M. & Garman, E.F. (2015) Identifying and quantifying radiation damage at the atomic level J. Synchrotron Radiat., 22(2):201-212
Osborne, J.M., Bernabeu, M.O., Bruna, M., Calderhead, B., Cooper, J., Dalchau, N., Dunn, S.J., Fletcher, A.G., Freeman, R., Groen, D., Knapp, B., McInerny, G.J., Mirams, G.R., Pitt-Francis, J., Sengupta, B., Wright, D.W., Yates, C.A., Gavaghan, D.J., Emmott, S. & Deane, C.M. (2014) Ten Simple Rules for Effective Computational Research PLoS Comput. Biol., 10(3):e1003506
Ali, W., Rito, T., Reinert, G., Sun, F. & Deane, C.M. (2014) Alignment-free protein interaction network comparison Bioinformatics, 30(17):i430-i437
Wilman, H.R., Ebejer, J.P., Shi, J., Deane, C.M. & Knapp, B. (2014) Crowdsourcing Yields a New Standard for Kinks in Protein Helices. J. Chem. Inf. Model., 54(9):2585-2593
Bradley, A.R., Wall, I.D., Green, D.V.S., Deane, C.M. & Marsden, B.D. (2014) OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data J. Chem. Inf. Model., 54(10):2636-2646
Dien, H., Deane, C.M. & Knapp, B. (2014) Gro2mat: A package to efficiently read gromacs output in MATLAB J. Comput. Chem., 35(20):1528-1531
Dunbar, J., Knapp, B., Fuchs, A., Shi, J. & Deane, C.M. (2014) Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design PLoS Comput Biol, 10:e1003852
Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi, J. & Deane, C.M. (2014) SAbDab: the structural antibody database Nucleic Acids Res., 42(Database issue):D1140--D1146
Kelm, S., Vangone, A., Choi, Y., Ebejer, J.P., Shi, J. & Deane, C.M. (2014) Fragment-based modeling of membrane protein loops: successes, failures, and prospects for the future Proteins, 82(2):175-186
Knapp, B., Dunbar, J. & 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 Comput Biol, 10(8):e1003748
Krawczyk, K., Liu, X., Baker, T., Shi, J. & Deane, C.M. (2014) Improving B-cell epitope prediction and its application to global antibody-antigen docking Bioinformatics, 30(16):2288-2294
Wilman, H.R., Shi, J. & Deane, C.M. (2014) Helix kinks are equally prevalent in soluble and membrane proteins. Proteins, 82(9):1960-70
Choi, Y., Agarwal, S. & Deane, C.M. (2013) How long is a piece of loop? PeerJ, 1
Ebejer, J.P., Fulle, S., Morris, G.M. & Finn, P.W. (2013) The emerging role of cloud computing in molecular modelling J. Mol. Graph. Model., 44:177-187
Luo, Q., Hamer, R., Reinert, G. & Deane, C.M. (2013) Local Network Patterns in Protein-Protein Interfaces PLoS One, 8(3):e57031
Zheng, S., Moehlenbrink, J., Lu, Y.C., Zalmas, L.P., Sagum, C.A., Carr, S., McGouran, J.F., Alexander, L.T., Fedorov, O., Munro, S., Kessler, B., Bedford, M.T., Yu, Q. & La Thangue, N.B. (2013) Arginine methylation-dependent reader-writer interplay governs growth control by E2F-1 Mol. Cell, 52(1):37-51
Hill, J.R. & Deane, C.M. (2013) MP-T: improving membrane protein alignment for structure prediction Bioinformatics, 29(1):54-61
Dunbar, J., Fuchs, A., Shi, J. & Deane, C.M. (2013) ABangle: characterising the VH–VL orientation in antibodies Protein Eng. Des. Sel., 26(10):611-620
Ebejer, J.P., Hill, J.R., Kelm, S., Shi, J. & Deane, C.M. (2013) Memoir: template-based structure prediction for membrane proteins Nucleic Acids Res., 41(Web Server issue):W379--W383
Edwards, H., Abeln, S. & Deane, C.M. (2013) Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies PLoS Comput Biol, 9(11):e1003325
Harrington, L., Cheley, S., Alexander, L.T., Knapp, S. & Bayley, H. (2013) Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate Proc. Natl. Acad. Sci., 110(47):E4417--E4426
Hischenhuber, B., Havlicek, H., Todoric, J., Höllrigl-Binder, S., Schreiner, W. & Knapp, B. (2013) Differential Geometric Analysis of Alterations in MH \alpha-Helices J. Comput. Chem., 34(21):1862-1879
Kelm, S., Choi, Y. & Deane, C.M.; Kasabov, N. (eds). (2013) Protein Modelling and Structural Prediction In Springer Handb. Bio-/Neuro-informatics
Knapp, B., Dorffner, G. & Schreiner, W. (2013) Early Relaxation Dynamics in the LC 13 T Cell Receptor in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study PLoS One, 8(6):e64464
Krawczyk, K., Baker, T., Shi, J. & Deane, C.M. (2013) Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking Protein Eng. Des. Sel., 26(10):621-629
Lori, C., Lantella, A., Pasquo, A., Alexander, L.T., Knapp, S., Chiaraluce, R. & 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
Ebejer, J.P., Morris, G.M. & Deane, C.M. (2012) Freely Available Conformer Generation Methods: How Good Are They? J. Chem. Inf. Model., 52(5):1146-1158
Gomes, M., Hamer, R., Reinert, G. & Deane, C.M. (2012) Mutual information and variants for protein domain-domain contact prediction BMC Res. Notes, 5(1):472
Kashir, J., Konstantinidis, M., Jones, C., Lemmon, B., Chang Lee, H., Hamer, R., Heindryckx, B., Deane, C.M., De Sutter, P., Fissore, R.A., Parrington, J., Wells, D. & Coward, K. (2012) A maternally inherited autosomal point mutation in human phospholipase C zeta (PLC\zeta) leads to male infertility Hum. Reprod., 27(1):222-231
Lewis, A.C.F., Jones, N.S., Porter, M.A. & Deane, C.M. (2012) What Evidence Is There for the Homology of Protein-Protein Interactions? PLoS Comput Biol, 8(9):e1002645
Mann, M., Saunders, R., Smith, C., Backofen, R. & Deane, C.M. (2012) Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains Adv. Bioinformatics, 2012:e148045
Pawelczyk, S., Scott, K.A., Hamer, R., Blades, G., Deane, C.M. & Wadhams, G.H. (2012) Predicting Inter-Species Cross-Talk in Two-Component Signalling Systems PLoS One, 7(5):e37737
Rito, T., Deane, C.M. & Reinert, G. (2012) The importance of age and high degree, in protein-protein interaction networks J. Comput. Biol. A J. Comput. Mol. Cell Biol., 19(6):785-795
Withers-Martinez, C., Suarez, C., Fulle, S., Kher, S., Penzo, M., Ebejer, J.P., Koussis, K., Hackett, F., Jirgensons, A., Finn, P. & Blackman, M.J. (2012) Plasmodium subtilisin-like protease 1 (SUB1): Insights into the active-site structure, specificity and function of a pan-malaria drug target Int. J. Parasitol., 42(6):597-612
Ali, W., M., D.C. & Reinert, G.; Stumpf, M., Balding, D.J. & Girolami, M. (eds). (2011) Protein interaction networks and their statistical analysis In Handb. Statistical Systems Biology
Choi, Y. & Deane, C.M. (2011) Predicting antibody complementarity determining region structures without classification Mol. Biosyst., 7(12):3327-3334
Deane, C.M. & Saunders, R. (2011) The imprint of codons on protein structure Biotechnol. J., 6(6):641-649
Saunders, R., Mann, M. & Deane, C.M. (2011) Signatures of co-translational folding Biotechnol. J., 6(6):742-751
Hill, J.R., Kelm, S., Shi, J. & Deane, C.M. (2011) Environment specific substitution tables improve membrane protein alignment. Bioinformatics, 27(13):i15-23
Agarwal, S., Deane, C.M., Porter, M.A. & Jones, N.S. (2010) Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks PLoS Comput. Biol., 6(6):e1000817
Ali, W. & Deane, C.M. (2010) Evolutionary analysis reveals low coverage as the major challenge for protein interaction network alignment Mol. Biosyst., 6(11):2296-2304
Ellis, J.J., Huard, F.P.E., Deane, C.M., Srivastava, S. & Wood, G.R. (2010) Directionality in protein fold prediction. BMC Bioinformatics, 11(1):172
Kelm, S., Shi, J. & Deane, C.M. (2010) MEDELLER: homology-based coordinate generation for membrane proteins Bioinformatics, 26(22):2833-2840
Saunders, R. & Deane, C.M. (2010) Protein structure prediction begins well but ends badly Proteins, 78(5):1282-1290
Choi, Y. & Deane, C.M. (2010) FREAD revisited: Accurate loop structure prediction using a database search algorithm Proteins, 78(6):1431-1440
Hamer, R., Chen, P.Y., Armitage, J.P., Reinert, G. & Deane, C.M. (2010) Deciphering chemotaxis pathways using cross species comparisons BMC Syst. Biol., 4:3
Hamer, R., Luo, Q., Armitage, J.P., Reinert, G. & Deane, C.M. (2010) i-Patch: interprotein contact prediction using local network information Proteins, 78(13):2781-2797
Lance, B.K., Deane, C.M. & Wood, G.R. (2010) Exploring the potential of template-based modelling Bioinformatics, 26(15):1849-1856
Lewis, A.C.F., Jones, N.S., Porter, M.A. & Deane, C.M. (2010) The function of communities in protein interaction networks at multiple scales BMC Syst. Biol., 4(1):100
Lewis, A.C.F., Saeed, R. & Deane, C.M. (2010) Predicting protein-protein interactions in the context of protein evolution Mol. Biosyst., 6(1):55-64
Rito, T., Wang, Z., Deane, C.M. & Reinert, G. (2010) How threshold behaviour affects the use of subgraphs for network comparison Bioinformatics, 26(18):i611--i617
Saunders, R. & Deane, C.M. (2010) Synonymous codon usage influences the local protein structure observed Nucleic Acids Res., 38(19):6719-6728
Kelm, S., Shi, J. & Deane, C.M. (2009) iMembrane: homology-based membrane-insertion of proteins. Bioinformatics, 25(8):1086-8
Ali, W. & Deane, C.M. (2009) Functionally guided alignment of protein interaction networks for module detection Bioinformatics, 25(23):3166-3173
Heytens, E., Parrington, J., Coward, K., Young, C., Lambrecht, S., Yoon, S.Y., Fissore, R.A., Hamer, R., Deane, C.M., Ruas, M., Grasa, P., Soleimani, R., Cuvelier, C.A., Gerris, J., Dhont, M., Deforce, D., Leybaert, L. & De Sutter, P. (2009) Reduced amounts and abnormal forms of phospholipase C zeta (PLCzeta) in spermatozoa from infertile men Hum. Reprod., 24(10):2417-2428
Patel, P.C., Fisher, K.H., Yang, E.C.C., Deane, C.M. & Harrison, R.E. (2009) Proteomic Analysis of Microtubule-associated Proteins during Macrophage Activation Mol. Cell. Proteomics, 8(11):2500-2514
Chen, P.Y., Deane, C.M. & Reinert, G. (2008) Predicting and validating protein interactions using network structure PLoS Comput. Biol., 4(7):e1000118
Fisher, K.H., Deane, C.M. & Wakefield, J.G. (2008) The functional domain grouping of microtubule associated proteins Commun Integr Biol, 1(1):47-50
Hughes, J.R., Meireles, A.M., Fisher, K.H., Garcia, A., Antrobus, P.R., Wainman, A., Zitzmann, N., Deane, C., Ohkura, H. & Wakefield, J.G. (2008) A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis PLoS Biol., 6(4)
Mann, M., Maticzka, D., Saunders, R. & Backofen, R. (2008) Classifying proteinlike sequences in arbitrary lattice protein models using LatPack HFSP J., 2(6):396-404
Saeed, R. & Deane, C. (2008) An assessment of the uses of homologous interactions Bioinformatics, 24(5):689-695
Valeyev, N.V., Downing, A.K., Sondek, J. & Deane, C. (2008) Electrostatic and functional analysis of the seven-bladed WD beta-propellers Evol. Bioinform. Online, 4:203-216
Abeln, S. & Deane, C. (2007) Linking evolution of protein structures through fragments BMC Syst. Biol., 1(Suppl 1):S12
Abeln, S., Teubner, C. & Deane, C.M. (2007) Using Phylogeny to Improve Genome-Wide Distant Homology Recognition PLoS Comput. Biol., 3(1)
Chen, P.Y., Deane, C.M. & Reinert, G. (2007) A statistical approach using network structure in the prediction of protein characteristics Bioinformatics, 23(17):2314-2321
Deane, C.M., Dong, M., Huard, F.P.E., Lance, B.K. & Wood, G.R. (2007) Cotranslational protein folding--fact or fiction? Bioinformatics, 23(13):i142-8
Saeed, R. & Deane, C.M. (2006) Protein protein interactions, evolutionary rate, abundance and age BMC Bioinformatics, 7(1):128
Huard, F.P.E., Deane, C.M. & Wood, G.R. (2006) Modelling sequential protein folding under kinetic control In Bioinformatics, 22(14)
Abeln, S. & Deane, C.M. (2005) Fold usage on genomes and protein fold evolution Proteins, 60(4):690-700
Winstanley, H.F., Abeln, S. & Deane, C.M. (2005) How old is your fold? Bioinformatics, 21 Suppl 1:i449--458
O'Leary, J.M., Hamilton, J.M., Deane, C.M., Valeyev, N.V., Sandell, L.J. & Downing, A.K. (2004) Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA J. Biol. Chem., 279(51):53857-53866