Selected Publications
Offman MN, Fitzjohn PW and Bates PA. Developing a move-set for protein model refinement. Bioinformatics, e-published 16 May 2006, doi:10.1093/bioinformatics/btl192. PubMed
Jonsson PF, Cavanna T, Zicha D and Bates PA. Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics 2006; 7: 2. PubMed PDF (UKPMC)
Smith GR, Fitzjohn PW, Page CS and Bates PA. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 2005: 60: 263-268. PubMed
Smith GR, Sternberg MJE and Bates PA. 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 2005; 347: 1077-1101. PubMed
Contreras-Moreira B, Fitzjohn PW and Bates PA. In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J Mol Biol 2003; 328: 593-608. PubMed
Primary Research Publications
2009
Patel N, Krishnan S, Offman MN, Krol M, Moss CX, Leighton C, van Delft FW, Holland M, Liu J, Alexander S, Dempsey C, Ariffin H, Essink M, Eden TO, Watts C, Bates PA, Saha V. A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase. J Clin Invest 2009 Jul;119(7):1964-73. doi: 10.1172/JCI37977. Epub 2009 Jun 8
2008
Bentley K, Gerhardt H, Bates PA. Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation. J Theor Biol 2008;250(1):25-36
Offman MN, Tournier AL, Bates PA. Alternating evolutionarypressure in a genetic algorithm facilitates protein model selection. BMC Struct Biol. 2008;8:34
Schmierer B,Tournier AL, Bates PA, Hill CS. Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proc Natl Acad Sci U S A. 2008;105(18):6608-13
2007
Krol M, Chaleil RAG, Tournier AT, Bates PA. Implicit flexibility in protein docking: Cross-docking and local refinement. Proteins 2007; 69(4):750-757
Krol M, Tournier AL, Bates PA. Flexible relaxation of rigid-body docking solutions. Proteins 2007; 68(1):159-169
2006
Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJE. The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci 2006; 361(1467):441-451
Jonsson PF, Bates PA. Global topological features of cancer proteins in the human interactome. Bioinformatics 2006; 22(18):2291-2297
Jonsson PF, Cavanna T, Zicha D, Bates PA. Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics 2006; 7:Article 2
Krol M, Wrona M, Page CS, Bates PA. Macroscopic pK(a) calculations for fluorescein and its derivatives. J Chem Theory Comput 2006; 2(6):1520-1529
Offman MN, Fitzjohn PW, Bates PA. Developing a move-set for protein model refinement. Bioinformatics 2006; 22(15):1838-1845
Page CS, Bates PA. Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? J Comput Chem 2006; 27(16):1990-2007
Rickman C, Jimenez JL, Graham ME, Archer DA, Soloviev M, Burgoyne RD, Davletov B. Conserved prefusion protein assembly in regulated exocytosis. Mol Biol Cell 2006; 17(1):283-294
Tournier AL, Fitzjohn PW, Bates PA. Probability-based model of protein-protein interactions on biological timescales. Algorithms Mol Biol 2006; 1:Article 25
Tournier AL, Fitzjohn PW, Bates PA. Probability-based model of protein-protein interactions on biological timescales. Algorithms Mol Biol 2006; 1:25
2005
Jimenez JL. Does structural and chemical divergence play a role in precluding undesirable protein interactions? Proteins 2005; 59(4):757-764
Smith GR, Fitzjohn PW, Page CS, Bates PA. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 2005; 60(2):263-268
Smith GR, Sternberg MJE, Bates PA. 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 2005; 347(5):1077-1101
2004
Fleming K, Muller A, MacCallum RM, Sternberg MJE. 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Res 2004; 32(Spec Iss):D245-D250
Mayor LR, Fleming KP, Muller A, Balding DJ, Sternberg MJE. Clustering of protein domains in the human genome. J Mol Biol 2004; 340(5):991-1004
Randall RA, Howell M, Page CS, Daly A, Bates PA, Hill CS. Recognition of phosphorylated-Smad2-containing complexes by a novel Smad interaction motif. Mol Cell Biol 2004; 24(3):1106-1121
Smith GR, Contreras-Moreira B, Zhang XD, Bates PA. A link between sequence conservation and domain motion within the AAA+ family. J Struct Biol 2004; 146(1-2):189-204
2003
Contreras-Moreira B, Fitzjohn PW, Bates PA. in silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J Mol Biol 2003; 328(3):593-608
Contreras-Moreira B, Fitzjohn PW, Offman M, Smith GR, Bates PA. Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space. Proteins 2003; 53(6 Supp 6):424-429
Contreras-Moreira B, Johnsson PF, Bates PA. Structural context of exons in protein domains: implications for protein modelling and design. J Mol Biol 2003; 333(5):1045-1059
Cootes AP, Muggleton SH, Sternberg MJE. The automatic discovery of structural principles describing protein fold space. J Mol Biol 2003; 330(4):839-850
Faraldo-Gomez JD, Smith GR, Sansom MSP. Molecular dynamics simulations of the bacterial outer membrane protein FhuA: a comparative study of the ferrichrome-free and bound states. Biophys J 2003; 85(3):1406-1420
Fitzjohn PW, Bates PA. Guided docking: first step to locate potential binding sites. Proteins 2003; 52(1):28-32
Jimenez JL, Smith GR, Contreras-Moreira B, Sgouros JG, Meunier FA, Bates PA, Schiavo G. Functional recycling of C2 domains throughout evolution: a comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches. J Mol Biol 2003; 333(3):621-639
Sellar GC, Watt KP, Rabiasz GJ, Stronach EA, Li L, Miller EP, Massie CE, Miller J, Contreras-Moreira B, Scott D, Brown I, Williams AR, Bates PA, Smyth JF, Gabra H. OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer. Nat Genet 2003; 34(3):337-343
Smith GR, Sternberg MJE. Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial. Proteins 2003; 52(1):74-79
2002
Alves R, Chaleil RAG, Sternberg MJE. Evolution of enzymes in metabolism: a network perspective. J Mol Biol 2002; 320(4):751-770
Contreras-Moreira B, Bates PA. Domain fishing: a first step in protein comparative modelling. Bioinformatics 2002; 18(8):1141-1142
Contreras-Moreira B, Fitzjohn PW, Bates PA. Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era. Appl Bioinformatics 2002; 1(4):177-190
Duncan T, Trewick SC, Koivisto P, Bates PA, Lindahl T, Sedgwick B. Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci U S A 2002; 99(26):16660-16665
Faraldo-Gomez JD, Smith GR, Sansom MSP. Setting up and optimization of membrane protein simulations. Eur Biophys J 2002; 31(3):217-227
Muller A, MacCallum RM, Sternberg MJE. Structural characterization of the human proteome. Genome Res 2002; 12(11):1625-1641
Randall RA, Germain S, Inman GJ, Bates PA, Hill CS. Different Smad2 partners bind a common hydrophobic pocket in Smad2 via a defined proline-rich motif. EMBO J 2002; 21(1-2):145-156
Other Publications
Sedgwick B, Bates PA, Paik J, Jacobs SC, Lindahl T. Repair of alkylated DNA: recent advances. DNA Repair 2007; 6(4):429-442
Ozdemir A, Masumoto H, Fitzjohn P, Verreault A, Logie C. Histone H3 lysine 56 acetylation: a new twist in the chromosome cycle. Cell Cycle 2006; 5(22):2602-2608
Davletov B, Jimenez JL. Sculpting a domain by splicing. Nat Struct Mol Biol 2004; 11(1):4-5
Moreira BC. Crystal: clear difference from glass. Nature 2003; 423(6943):917-918
Smith GR, Sternberg MJE. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002; 12(1):28-35
