Bates PA, McGregor MJ, Islam SA, Sattentau QJ, Sternberg MJE (1989). A predicted three-dimensional structure for the human immunodeficiency virus binding domains of CD4 antigen. Prot. Eng., 3, 13-21.
McGregor, MJ, Bates, PA, Islam SA, Sternberg MJE, Sattentau QJ (1990). A predicted three-dimensional structure of CD4 and the location of the HIV gp120 binding region. In Protein Engineering-Protein Design in Basic Research, Medicine, and Industry, (ed. M.Ikehara, T.Oshima and K.Titani), pp. 83-85. Japan Scientific Societies Press, Tokyo.
Hogg N, Bates PA, Harvey J. (1991) Structure and function of intercellular adhesion molecule-1. Chemical Immunology, 50, 98-115.
Nelson RW, Bates PA, Rutishauser U, Protein determinants for specific polysialylation of the neural cell-adhesion molecule. J. Biol. Chem. 1995, Vol: 270 (29), P: 17171-17179
Bates PA, Berendt A, Bennett R, Cabanas C, Craig A, Harvey J, McDowall A, Hogg N (1992), Leukocyte integrin activation. Pathologie Biologie, Vol: 40 (8), P: 785-788
Berendt AR, McDowall A, Craig AG, Bates PA, Sternberg MJE, Marsh K, Newbold CI, Hogg N (1992). The binding site on ICAM-1 for Plasmodium falciparum-infected erythrocytes overlaps, but is distinct from, the LFA-1 binding site. Cell, Vol: 68, p: 71-81
Saqi MAS, Bates PA, Sternberg MJE (1992). Towards an automatic method of predicting protein-structure by homology - an evaluation of suboptimal sequence alignments. Protein Eng., Vol: 5 (4), P: 305-311
Bates PA, Luo JC, Sternberg MJE (1992), A predicted 3-dimensional structure for the carcinoembryonic antigen (cea). FEBS Lett., Vol: 301 (2), P: 207-214
Luo JC, Bates PA, Sternberg MJE. (1992). A predicted three-dimensional structure for the carcinoembryonic antigen (CEA). In Peptides. Biology and Chemistry. Proceedings of the 1992 Chinese Peptide Symposium, (ed. Du, Y.-c., Tam, J.P. and Zhang, Y.-s.), pp. 115-119. ESCOM, Leiden.
Bates PA, Sternberg MJE. (1992). From protein sequence to structure. In Protein Engineering-A Practical Approach, (ed. Rees, A.R., Sternberg, MJE and Wetzel, R.), pp. 117-141. Oxford University Press, Oxford.
Berendt AR, Craig AG, McDowall A, Bates PA, Roberts DJ, March K, Hogg N, Newbold CI (1992). Interactions of malaria-infected erythrocytes with ICAM-1. In Leukocyte Adhesion Basic and Clinical Aspects, (ed. Gahmberg CG, Mandrup-Poulsen T, Wogensen Bach L, Hokfelt B), pp 271-285. Excerpta Medica, Amsterdam.
Berendt AR, McDowall A, Craig AG, Bates PA, Newbold CI, Hogg N (1993). Interactions of the Plasmodium falciparum-infected erythrocyte with ICAM-1. In Structure, Function and Regulation of Molecules involved in Leukocyte Adhesion, (ed. Lipsky, PE, Rothlein R, Kishimoto TK, Faanes RB, Smith CW), pp 92-103. Springer-Verlag, New York.
Bates PA, Islam SA, Sternberg MJE (1993), Structure of debrisoquinium sulfate. Acta Crystallographica Section C-crystal Structure Communications, Vol: 49 (eb), P: 300-303
Stanley P, Bates PA, Harvey J, Bennett RI, Hogg N (1994), Integrin lfa-1 alpha-subunit contains an icam-1 binding-site in domain-v and domain-vi. EMBO J., Vol: 13 (8), P: 1790-1798
Hogg N, Landis RC, Bates PA, Stanley P, Randi AM (1994), The sticking point: how integrins bind to their ligands. Trends Cell Biol., Vol 4, p:379-382
Luo JC, Liu Q, Coombers CR, Bates PA, Sternberg MJE, (1994). Prediction of the three-dimensional structure of activin. In Peptides Biology and Chemistry. Proceedings of the 1994 Chinese Peptide Symposium, (ed. Lu, G., Tam, J.P., and Cai, M.) ESCOM, Leiden.
Holness CL, Bates PA, Littler AJ, Buckley CD, McDowall A, Bossy D, Hogg N, Simmons DL (1995), Analysis of the binding site on intercellular adhesion molecule 3 for the leukocyte integrin lymphocyte functionassociated antigen 1. J. Biol. Chem., vol: 270 (2), p:877-884
Watt SM, Gschmeissner SE, Bates PA (1995), Pecam-1 - its expression and function as a cell-adhesion molecule on hematopoietic and endothelial-cells. Leukemia & Lymphoma, Vol: 17 (3-4), P: 229-244
Chinery R, Bates PA, De A, Freemont PS (1995). Characterization of the single-copy trefoil peptides intestinal trefoil factor and ps2 and their ability to form covalent dimers. FEBS Lett., Vol: 357(1), P: 50-54
Bates PA, Jackson RM, Sternberg MJE (1996). Prediction of protein structures and their docking. In Genomes Molecular Biology and Drug Discovery, (ed. Browne MJ and Thurlby PL), pp 73-86. Academic Press.
Russell R.B., Saqi M.A.S., Sayle R.A., Bates P.A., Sternberg M.J.E. (1997). Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol. 269: 423-439.
Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJE. (1997). An Automated classification of the structure of protein loops. J. Mol. Biol. 266: 814-830.
Dokurno P, Lally JM, Bates PA, Band HA, Snary D, Freemont PS (1997). Crystallization of the Fab fragment of the tumour-specific antibody PR1A3. Acta Cryst. D53: 472-473.
Dokurno P, Lally JM, Bates PA, Taylor-Papadimitriou J, Band HA, Snary D, Freemont PS (1997). Crystallization of an antitumour antibody SM3 complexed with a peptide epitope. Acta Cryst. D53: 780-781.
Bates PA, Jackson RM, Sternberg MJE. (1997). Model building by comparison: a combination of expert knowledge and computer automation. Proteins, Suppl. 1: 59-67.
Bodmer WF, Durbin H, Snary D, Stewart LM, Young S, Bates PA. (1994). Monoclonal Antibodies (patent): PR1A3 a colorectal cancer antibody: GB9317423.3
Russell, R.B., Saqi, M.A.S., Bates, P.A., Sayle R.A. & Sternberg, M.J.E. (1998). Recognition of analogous and homologous protein folds- assessment of prediction success and associated alignment accuracy using empirical substitution matrices. Prot. Eng., 11, 1-9
Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJE. (1998). Automated classification of antibody complementarity determining region 3 of the heavy chain (CDR-H3) loops into canonical forms. J. Mol. Biol. 279, 1193-1210.
McDowall A, Leitinger B, Stanley P, Bates PA, Randi AM, Hogg N. (1998). The I domain of integrin LFA-1 is involved in a conformational change leading to high affinity binding to ligand ICAM-1. J. Biol. Chem. 273, 42, 27396-27403.
Bates PA, Dokurno, P, Freemont PS, Sternberg MJE (1998). Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementary determining region (CDR) of an antibody. J. Mol. Biol. 284: 549-555.
Dokurno P, Bates PA, Band HA, Stewart LMD, Lally JM, Burchell JM, Taylor-Papadimitriou J, Snary D, Sternberg MJE, Freemont PS (1998). Crystal structure at 1.95A resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition. J. Mol. Biol. 284: 713-728.
Freemont PS, Bates PA, Dokurno P, Sternberg MJE. (1998). Novel Chemical Entity (SM3-MUC1 crystal patent): GB 9802542
Zhang X, Morera S, Bates PA, Whitehead PC, Coffer AI, Hainbucher K, Nash RA, Sternberg MJE, Lindahl T, Freemont PS. (1998). Structure of an XRCC1 BRCT domain: a new protein-protein interaction module. EMBO J. 17, 6404-6411.
Constantinou A, Gunz D, Evans E, Lalle P, Bates PA, Wood RD, Clarkson SG. (1999). Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair. J. Biol. Chem. 26;274(9): 5637-5648.
Stewart LM, Young S, Watson G, Mather SJ, Bates PA, Band HA, Wilkinson RW, Ross EL, Snary D. (1999). Humanisation and characterisation of PR1A3, a monoclonal antibody specific for cell-bound carcinoembryonic antigen. Cancer Immunol. Immunother. 47: 299-306.
Bates PA, Sternberg MJE (1999). Model building by comparison at CASP3: using expert knowledge and computer automation. Proteins, Suppl. 3: 47-54.
Sternberg MJE, Bates PA, Kelley LA, MacCallum RM. (1999). Progress in protein structure prediction: assessment of CASP3. Curr. Opin. Struc. Biol. 9: 368-373.
Sternberg, M.J.E., Bates, P.A., Gabb, H.A., Jackson, R.M., Kelley, L.A., MacCallum, R.M., Moont, G. & Muller, A. (2000). Structural Bioinformatics in the post genome era. In Sequence Analysis in the Genome Era. (ed. Casadio, R., Masotti, L.), CLUEB, Bologna, Italy (in press).
Hogg, N. & Bates, P.A. (2000). Genetic analysis of integrin function in man: LAD-1 and other syndromes. Matrix Biol. 19(3): 211-222.
Huyton, T., Bates, P.A., Zhang, X., Sternberg, M.J.E. & Freemont, P.S. (2000). The BRCA1 C-Terminal (BRCT) domain: structure and function. Mutat. Res. 460(3-40): 319-332.
Stanley, P., McDowall, A., Bates, P.A., Brashaw, J. & Hogg, N. (2000). The second domain of intercellular adhesion molecule-1 (ICAM-1) maintains the structural integrity of the leucocyte function-associated antigen-1 (LFA-1) ligand-binding site in the first domain. Biochem. J., 351, 79-86.
Zhang, X., Shaw, A., Bates, P.A., Newman, R.H., Gowen, B., Orlova, E., Gorman, M.A., Kondo, H., Dokurno, P., Lally, J., Leonard, G., Meyer, H., van Heel, M., Freemont, P.S. (2000). Structure of the AAA ATPase p97. Molecular Cell, 6, 1473-1484.
Bates, P.A., Kelley, L.A., MacCallum, R.M. & Sternberg, M.J.E. (2001). Enhancement of Protein Modelling by Human Intervention in Applying the Automatic Programs 3D-JIGSAW and 3D-PSSM. Proteins, Suppl. 5: 39-46.
Dulic, A., Bates, P.A., Zhang, X., Martin, S.R., Freemont, P.S., Lindahl, T. & Barnes, D.E. (2001). BRCT domain interacts in the heterodimeric DNA repair protein XRCC1-DNA ligase III. Biochemistry, 40, 5906-5913.
Watt, S.M., Teixeira, A.M., Zhou, G.Q., Doyonnas, R., Zhang, Y., Grunert, F., Blumberg, R.S., Kuroki, M., Skubitz, K.M., & Bates, P.A. (2001). Homophilic Adhesion of Human CEACAM1 Involves N-Terminal Domain Interactions: Structural Analysis of the Binding Site. Blood, 98, 1469-1479.
Hilkens, C.M.U., Is'harc H., Lillemeier, B.F., Strobl, B., Bates P.A., Behrmann, I & Kerr, I.M. (2001). A region encompassing the FERM domain of Jak1 is nessessary for binding to the cytokine receptor gp130. FEBS Lett., Vol: 505 (2), P: 87-91
Randall, R.A., Germain, S., Inman, G.J., Bates, P.A. & Hill, C.S. (2002). The molecular basis for Smad2-transcription factor interactions. EMBO J., 21, 145-156.
Contreras-Moreira, B., Bates, P.A. (2002). Domain Fishing: a first step in protein comparative modelling. Bioinformatics, 18, 1141-1142.
Contreras-Moreira,B. , Bates,P.A. (2002). Domain Fishing and 3D-JIGSAW, web tools for protein comparative modelling. In de Las Rivas,J.,ed.Proceedings of the Symposium on Bioinformatics and Computational Biology 2002: 95.
Duncan, T., Trewick, S.C., Koivisto, P., Bates, P.A., Lindahl, T., Sedgwick, B. (2002). Reversal of DNA alkylation damage by two human dioxygenases. PNAS ,99,16660-16665.
Contreras-Moreira, Fitzjohn P.W. & Bates P.A. (2002). Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era. Applied Bioinformatics , 1(4), 177-190.
Contreras-Moreira B., Fitzjohn P.W., Offman M., Smith G.R. & Bates P.A. (2003). Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space. Proteins, 53, 424-429.
Fitzjohn, P.W., Bates, P.A. (2003). Guided Docking: A First Step to Locate Potential Binding Sites. Proteins, 52(1), 28-32.
Contreras-Moreira B., Fitzjohn P.W. & Bates P.A. (2003). In silico Protein Recombination: enhancing template and sequence alignment selection for comparative protein modelling. J. Mol. Biol. 328, 593-608.
Sellar G.C., Watt K.P., Rabiasz G.J., Stronach E.A., Li L., Miller E.P., Massie C.E., Miller J, Contreras-Moreira B., Scott D., Brown I., Williams A.R., Bates P.A., Smyth J.F. & Gabra H. (2003). OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer. Nature Genetics,34: 337-343.
Jimenez, J.L., Smith, G.R., Contreras-Moreira, B., Sgouros, J.G., Meunier, F.A., Bates P.A. & Schiavo, G. (2003). A comparative study Of synaptotagmin, protein kinase C and phosholipase C by sequence, structural and modelling approaches. J. Mol. Biol. 333, 621-639.
Contreras-Moreira, B., Jonsson, P.F. & Bates P.A. (2003). Structural context of exons in protein domains: implications for protein modelling and design. J. Mol. Biol. 333, 1057-1071.
Randall, R.A., Howell, M., Page, C.S., Daly, A., Bates, P.A. & Hill, C.S. (2004). Recognition of phosphorylated Smad2-containing complexes by a novel Smad-interaction motif. Mol. Cell. Biol. 24, 1106-1121.
Smith, G.R., Contreras-Moreira, B., Zhang, X. & Bates, P.A. (2004). A Link Between Sequence Conservation and Domain Motion Within the AAA+ Family. J. Struct. Biol. 146, 189-204.
Smith, G.R., Fitzjohn, P.W., Page C.S. & Bates, P.A. (2005). Incorporation of Flexibility into Rigid-Body Docking: Applications in Rounds 3-5 of CAPRI. Proteins 60, 263-268.
Smith, G.R., Sternberg, M.J.E. & Bates, P.A. (2005). The Relationship Between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking. J. Mol. Biol. 347, 1077-1101.
Jonsson, P.F., Cavanna, T., Zicha, D. & Bates, P.A. (2006). Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics 7:2.
Offman, M.N., Fitzjohn, P.W.. & Bates, P.A. (2006). Developing a move-set for protein model refinement. Bioinformatics 22, 1838-1845.
Page, C.S., & Bates, P.A. (2006). Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? J. Comput. Chem. 27, 1990-2007.
Jonsson, P.F. & Bates, P.A. (2006). Global topological features of cancer proteins in the human interactome Bioinformatics 22, 2283-2290.
Krol, M., Wrona, M., Page, C.S. & Bates, P.A. (2006). Macroscopic pKa calculations for fluorescein and its derivatives. J. Chem. Theory Comput. 2, 1520-1529.
Tournier, A.L., Fitzjohn, P.W. & Bates, P.A. (2006). Probablility-based model of protein-protein interactions on biological timescales. Algorithms Mol. Biol. 1:25. Sedgwick, B., Bates, P.A., Paik, J., Jacobs, S.C. & Lindahl, T. (2007). Repair of alkylated DNA: recent advances. DNA Repair 6, 429-442.Krol, M., Tournier, A.L. & Bates, P.A. (2007). Flexible Relaxation of Rigid-Body Docking Solutions. Proteins: Structure, Function and Bioinformatics 68, 159-169.
Krol, M., Chaleil, R.A.G., Tournier, A.L. & Bates, P.A. (2007). Implicit flexibility in protein docking:cross-docking and local refinement. Proteins: Structure, Function and Bioinformatics 69, 750-757. Bentley, K., Gerhardt, H. & Bates, P.A. (2008). Agent-based simulation of notch mediated tip cell selection in angiogenic sprout initialisation. J. Theor. Biol. 250, 25-36. Schmierer, B., Tournier, A.L, Bates, P.A. & Hill, C.S. (2008). Mathematical modelling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. PNAS ,105,6608-6613. Offman, M.N., Tournier, A.L. & Bates, P.A. (2008). Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection. BMC Structural Biology 8:34. Patel, N., Krishnan, S., Offman, M.N., Krol, M., Moss, C.X., Leighton, C., van Delft, F.W., Holland, M., Liu, J., Alexander, S., Dempsey, C., Ariffin, H., Essink, M., Eden, T.O.B., Watts, C., Bates, P.A. & Saha, V. (2009). A dyad of lymphoblastic lysosomal cysteine proteases degrades the key anti-leukemic drug L-asparaginase. J. Clin. Invest. 119: 1964-1973 Krol, M., Tournier, A.L., & Bates, P.A. (2009). In-silico docking: predicting protein-protein interactions. In "Structure-Function Relation in Proteins", (Roterman, I., ed.),pp 1-43, Transworld Research Network, ISBN: 978-81-7895-409-7. Bentley, K., Mariggi, G., Gerhardt, H. & Bates, P.A. (2009). Tipping the balance: robustness of tip cell selection, migration and fusion in angiogenesis. PLoS Comput. Biol. 5(10):e1000549. Li, X.F, Moal, I.H. & Bates, P.A. (2010). Detection and refinement of encounter complexes for protein-protein docking: tacking account of macromolecular crowding. Proteins: Structure, Function and Bioinformatics. (in press). Kurkcuoglu, O. & Bates, P.A. (2010). Mechanism of cohesin loading onto chromosomes: a conformational dynamics study. Biophys. J. (accepted).