Publications


1997

  • Keinänen, K., Arvola, M., Kuusinen, A. and Johnson, M.S. (1997). Ligand recognition in glutamate receptors: insight from mutagenesis of the soluble alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-binding domain of glutamate receptor type D (GluR-D). Trans. Biochem. Soc. 25: 835-838
  • Wahlberg, M. and Johnson, M.S. (1997). Isolation and characterization of five actin cDNAs from the cestode Diphyllobothrium dendriticum - a phylogenetic study of the multigene family. J. Mol. Evol. 44: 159-168 Medline

1996

  • Denesyuk, A., Johnson, M.S., Zavyalov, V.P. and Korpela, T. (1996). Structure of Cytokine Hydrophobic Cores. J. Theor. Biol. 180: 297-307 Medline
  • Johnson, M.S., May, A.C.W., Rodionov, M.A. and Overington, J.P. (1996). Discrimination of common protein folds: applications of structural information to sequence/structure comparisons. Methods in Enzymology 266: 575-598 Medline
  • Johnson, M.S. (1996). Applications of Computing to Structural Molecular Biology. Proceedings of the Finnish Artificial Intelligence Society. 284-291

1995

  • May, A.C.W. and Johnson, M.S. (1995). Improved genetic algorithm-based protein structure comparisons: pairwise and multiple superpositions. Prot. Engineer. 8: 873-882 Medline
  • Johnson, M.S., Hoffrén, A.-M. and Cockcroft, V. (1995). Macromolecular modelling for the 21st Century. Kemia Kemi 22: 691-695
  • Johnson, M.S. (1995). Cornering and Capturing the Common Protein Fold. Trends in Molecular Medicine 1: 188-194 Medline

1994

  • Rodionov, M.A. and Johnson, M.S. (1994). Residue-residue contact substitution probabilities derived from aligned 3-D structures and the identification of common folds. Protein Science 3: 2366-2377
  • May, A.C. and Johnson, M.S. (1994). A method for the comparison of three-dimensional structures using a combination of genetic algorithms, dynamic programming and least-squares minimization. Protein Engineering 7: 475-485
  • May, A.C., Johnson, M.S., Blundell, T.L. et al (1994). The recognition of protein structure and function from sequence: adding extra value to genome data. Proc. Phil. Trans. R. Soc. Lond. B 244: 373-381
  • Johnson, M.S., Srinivasan, N., Sowdhamini, R. and Blundell, T.L. (1994). Knowledge-based Modelling. CRC Crit. Rev. Biochem. Molec. Biol. 29: 1-68
  • Johnson, M.S., Overington, J.P., Edwards, Y., May, A. and Rodionov, M.A. (1994). An integrated approach to the comparison of structures and sequences: alignment, searching and the detection of common folds. Proc. 27th Hawaii Intern. Conf. Syst. Sci. V: 296-305
  • Edwards, Y., Johnson, M.S., Moss, D.S. and Blundell, T.L. (1994). The effects of local environments on the pattern of amino-acid substitution in homologous structures: the role of side-chain to main -chain van der Walls interactions. In: Techniques in protein chemistry V, (Crabb, J.W. ed.) Academic Press, New York, pp.405-412

1993 and earlier

  • Shearer, A.C. and Johnson, M.S. (1993). Confidence limits on branching orders in phylogenetic tree construction. Protein Science 2: 1686-1696
  • Johnson, M.S. and Overington, J.P. (1993). A structural basis for the comparison of sequences: An evaluation of scoring methodologies. J. Mol. Biol. 233: 716-738
  • Blundell, T.L. and Johnson, M.S. (1993). Catching a common fold. Protein Science 2: 877-883
  • Johnson, M.S., Overington, J.P. and Blundell, T.L. (1993). Alignment and Searching for Common Folds Using a Data Bank of Structural Templates. J. Mol. Biol. 231: 735-752
  • Overington, J.P., Zhu, Z.-Y., Sali A., Johnson, M.S., Sowdhamini, R., Louie, G.V. and Blundell, T.L. (1993). Molecular recognition in protein families: a database of aligned 3-D structures of related proteins. Biochem. Soc. Symp. 21: 597-604
  • Johnson, M.S. and Blundell, T.L. (1993). Sequence patterns that characterize protein families with a common fold. In: Methods in Protein Sequence Analysis, Plenum, New York.
  • Johnson, M.S. (1993). From the comparison of proteins to homology-based modelling. In: Proceedings of the Second International Conference on Computer Applications to Materials and Molecular Science and Engineering - CAMSE"'"92, Elsevier Science Publishers, Espom, The Netherlands.
  • Hoffrén, A.-M., Saloheimo, M., Thomas, P., Overington, J.P., Johnson, M.S., Knowles, J.K.C. and Blundell T.L. (1993). Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure. Prot. Engin. 6: 177-182
  • Topham, C., McLeod, A., Eisenmenger, F., Overington, J.P., Johnson, M.S. and Blundell, T.L. (1993) Identification of key residues in structurally variable regions of proteins using conformationally-constrained environmental substitution tables: Applications to loop fragment ranking in modelling of protein structure. J. Mol. Biol. 229: 194-220
  • Overington, J.P., Donnelly D., Johnson, M.S., Sali A. and Blundell, T.L. (1992). Environmental specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Science 1: 216-226
  • Sali, A., Overington, J.P., Johnson, M.S. and Blundell, T.L. (1992). From modelling homologous proteins to prediction of structure. In: Computer Modelling of Biomolecular Processes, (J.M. Goodfellow and D.S. Moss, eds.) Ellis Horwood, London, pp.231-245
  • Johnson, M.S. (1991). From the comparative analysis of proteins to similarity-based modelling. In: Modelling and Computer Methods in Molecular Biology and Genetics, Nova Science Publishers, Commack, NY.
  • Hoffrén, A.-M., Saloheimo, M., Thomas, P., Overington, J.P., Johnson, M.S., Knowles, J.K.C. and Blundell T.L. (1991) Knowledge-based modelling of the lignin peroxidase LIII of Phlebia radiata. J. Chim. Phys. 88: 2659-2662
  • Blundell, T. et al (1991). Patterns of sequence variation in families of homologous proteins. In: Methods in Protein Sequence Analysis, (Jörnvall-Höög-Gustavson, eds.) Verlag, Basel, pp. 373-385
  • Johnson, M.S. (1991). Comparisons of proteins. Current Opinion in Structural Biology 1: 334-344
  • Topham, C., Thomas, P., Overington, J.P., Johnson, M.S., Eisenmenger, F. and Blundell, T.L. (1991). An assessment of COMPOSER: A rule-based approach to modelling protein structure. Biochem. Soc. Symp. 57: 1-9
  • Overington, J.P., Johnson, M.S., Sali, A. and Blundell, T.L. (1990). Tertiary constraints on protein evolutionary diversity: Templates, key residues and structural prediction. Proc. Roy. Soc. London B 241: 132-145
  • Overington, J.P., Johnson, M.S., Topham, C., McLeod, A., Sali, A., Zhu, Z.Y., Sibanda, L. and Blundell, T.L. (1990) Applications of environmental specific amino acid substitution tables to identification of key residues in protein structure. Current Science 59: 867-874
  • Johnson, M.S., Sutcliffe, M. J. and Blundell, T. L. (1990). Molecular Anatomy: Phyletic relationships derived from three dimensional structures of proteins. J. Mol. Evol. 30: 43-59
  • Johnson, M.S., Overington, J.P. and Sali, A. (1990). Knowledge-based protein modelling: Human plasma kallikrein and human neutrophil defensin. In: Current Research in Protein Chemistry. (J. Villafranca, ed.) Academic Press, New York, pp. 567-574
  • Johnson, M.S., Sali, A. and Blundell, T. L. (1990). Phylogenetic relationships from three-dimensional structures of proteins. Meth. Enzym. 183: 670-690
  • Blundell, T.L., Johnson, M.S., Overington, J.P. and Sali, A. (1990). Knowledge-based protein modelling and the design of novel molecules. In: Protein design and the development of new therapeutics and vaccines, (Hook and Poste, eds.) Plenum, New York, pp. 209-227
  • Johnson, M.S. et al. (1990). From the comparative structure analysis to protein engineering: knowledge-based modelling and design. Fresenius J. Anal. Chem. 337: 1-3
  • Doolittle, R.F., Feng, D.-F., McClure, M.A. and Johnson, M.S. (1990). Retrovirus phylogeny and evolution. Current Topics in Microbiology and Immunology 157: 1-18
  • Sali, A., Overington, J.P., Johnson, M.S. and Blundell, T.L. (1990). Knowledge-based protein modelling. TIBS 15: 235-240
  • Donnelly, D., Johnson, M.S., Blundell, T.L. and Saunders, J. (1989). An analysis of the periodicity of conserved residues in sequence alignments of G-protein coupled receptors. FEBS Letts. 251: 109-116
  • Blundell, T.L., Carney, D., Hubbard, T., Johnson, M.S., McLeod, A., Overington, J.P., Sali, A., Sutcliffe, M. and Thomas, P. (1989). Knowledge-based protein modelling and design. GBF Monographs 12: 39-43
  • Doolittle, R.F., Feng, D.-F., Johnson, M.S. and McClure, M.A. (1988). Origins and evolutionary relationships of retroviral proteins. Quarterly Review of Biology 64: 1-30
  • Nagel, G.M., Johnson, M.S., Rynd, J., Petrella, E. and Weber, B.H. (1988). Glycyl-tRNA synthetase of Escherichia coli: Immunological homology with phenylalanyl-tRNA synthetase. Arch. Biochem. Biophys. 262: 409-415
  • McClure, M.A., Johnson, M.S., Feng, D.-F. and Doolittle, R.F. (1988). Sequence comparisons of retroviral proteins: relative rates of change and general phylogeny. Proc. Natl. Acad. Sci. USA 85: 2469-2473
  • McClure, M.A., Johnson, M.S. and Doolittle, R.F. (1987). Relocation of a protease-like gene segment between two retroviruses. Proc. Natl. Acad. Sci. USA 84: 2693-2697
  • Doolittle, R.F., Feng, D.-F., Johnson, M.S. and McClure, M.A. (1987). Relationships of human protein sequences to those of other organisms. Cold Spring Harbor Symposia on Quantitative Biology. Vol. LI: 447-455
  • Johnson, M.S., McClure, M.A., Feng, D.-F., Gray, J. and Doolittle, R.F. (1986). Computer analysis of retroviral pol genes: assignment of enzymatic functions to specific sequences and homologies with nonviral enzymes. Proc. Natl. Acad. Sci. USA 83: 7648-7652
  • Doolittle, R.F., Johnson, M.S., Husain, I., Van Houtan, B., Thomas, D.C. and Sancar, A. (1986). Domainal evolution of a prokaryotic DNA-repair protein and its relationship to active transport proteins. Nature 323: 451-455
  • Johnson, M.S. and Doolittle, R.F. (1986). A method for the simultaneous alignment of three or more amino acid sequences. J. Mol. Evol. 23: 267-278
  • Fong, H.K.W., Hurley, J.B., Hopkins, R.S., Lye, R.M.-L., Johnson, M.S., Doolittle, R.F. and Simon, M.I. (1986). Repetitive segmental structure of the transducin beta subunit: homology with the CDC4 gene and identification of related mRNAs. Proc. Natl. Acad. Sci. USA 83: 2162-2166
  • Feng, D.-F., Johnson, M.S. and Doolittle, R.F. (1985). Aligning amino acid sequences: comparison of commonly used methods. J. Mol. Evol. 21: 112-125
  • Davidson, F.F. and Johnson, M.S. (1985). Biochemistry laboratory manual: protein chemistry. Department of Chemistry, University of California, San Diego.
  • Doolittle, R.F., Feng, D.-F. and Johnson, M.S. (1984). Computer-based characterization of epidermal growth factor precursor. Nature 307: 558-560
  • Nagel, G.M., Cumberledge, S., Johnson, M.S., Petrella, E. and Weber, B.H. (1984). The beta subunit of E. coli glycyl-tRNA synthetase plays a major role in tRNA recognition. Nucleic Acids Research 12: 4377-4384