Publications
Refereed...
1989
Martin, A. C. R., Cheetham, J. C. and Rees, A. R. (1989). Modelling antibody hypervariable loops: A combined algorithm. Proceedings of the National Academy of Science, 86,9269-9272. [PDF]
1992
Jackson, T., Morris, B. A., Martin, A. C. R., Lewis, D. F. V. and Sanders, P. G. (1992) Molecular modelling and site-directed mutagenesis on a bovine anti-testosterone monoclonal antibody. Protein Engineering, 5, 343-350. [PDF]
1993
Martin, A. C. R. (1993) MoG: Molecular graphics for the Commodore Amiga. Journal of Molecular Graphics, 11, 53-55. [PDF]
Gregory, D. St.J., Martin, A. C. R., Cheetham, J. C. and Rees, A. R. (1993) The prediction and characterization of metal binding sites in proteins. Protein Engineering, 6, 29-35. [PDF]
1995
Reczko, M., Martin, A. C. R., Bohr, H. and Suhai, S. (1995) Prediction of hypervariable CDR-H3 loop structures in antibodies. Protein Engineering, 8, 389-395. [PDF]
Martin, A. C. R., Toda, K., Stirk, H. J. and Thornton, J. M. (1995) Long loops in proteins. Protein Engineering, 8, 1093-1101 [PDF]
1996
Martin, A. C. R. (1996) Accessing the Kabat antibody sequence database by computer. PROTEINS: Structure, Function and Genetics, 25, 130-133 [PDF]
Kalsi, J. K., Martin, A. C. R., Hirabayashi, Y., Ehrenstein, M., Longhurst, C. M., Ravirajan, C., Zvelebil, M., Stollar, D., Thornton, J. M and Isenberg, D. A. (1996) Functional and modelling studies of the binding of Human monoclonal anti-DNA antibodies to DNA. Molecular Immunology, 33, 471-483 [PDF]
MacCallum, R. M., Martin, A. C. R. and Thornton, J. M. (1996) Antibody-antigen interactions: Contact analysis and binding site topography. J. Mol. Biol., 262, 732-745 [PDF]
Martin, A. C. R. and Thornton, J. M. (1996) Structural families of loops in homologous proteins: Automatic classification, modelling and application to antibodies. J. Mol. Biol., 263, 800-815 [PDF]
1997
Kipriyanov, S. M., Moldenhauer, G., Martin, A. C. R., Kupriyanova, O. A. and Little, M. (1997) Two amino acid mutations in an anti-human CD3 single chain Fv antibody fragment that affect the yield on bacterial secretion, but not the affinity. Protein Engineering, 10, 445-453 [PDF]
Martin, A. C. R., MacArthur, M. W. and Thornton, J. M. (1997) Assessment of Comparative Modelling in CASP2. PROTEINS: Structure, Function and Genetics, Suppl. 1, 14-28 [PDF]
1998
Ravirajan, C. T., Rahman, M. A., Papadaki, L., Griffiths, M., Kalsi, J., Martin, A. C. R., Ehrenstein, M. R., Latchman, D. S. and Isenberg, D. A. (1998) Genetic Structural and Functional Properties of a Human IgG Anti-DNA Antibody. European Journal of Immunology, 28, 339-350 [PDF]
Martin, A. C. R., Orengo, C. A., Hutchinson, E. G.,
Jones, S., Karmirantzou, M., Laskowski, R. A.,
Mitchell, J. B. O., Taroni, C. and Thornton, J. M. (1998)
Protein Folds and Functions.
Structure, 6, 875-884
Related Web pages
[PDF]
Zuccotto, F., Martin, A. C. R., Laskowski, R. A., Gilbert, I. and Thornton, J. M. (1998) Dihydrofolate Reductase: a Potential Drug Target in Trypanosomes and Leishmania. Journal of Computer Aided Molecular Design, 12, 241-257 [PDF]
Orengo, C. A., Martin, A. C. R., Hutchinson, G., Jones, S., Jones. D.J., Michie, A. D., Swindells, M. B., and Thornton, J. M. (1998) Classifying a protein in the CATH database of domain structures. Acta Crystallographica, D54, 1155-1167 [PDF]
1999
Liu, Z., Song, D., Kramer, A., Martin, A. C. R., Dandekar, T., Schneider-Mergener, J., Bautz, E. K. F. and Duebel, S. (1999) Fine mapping of the antigen-antibody interaction of scFv215, a recombinant antibody inhibiting RNA polymerase II from Drosophila melanogaster Journal of Molecular Recognition, 12, 103-111 [PDF]
Orengo, C. A., Pearl. F. M., Bray J. E., Todd, A. E., Martin. A. C. R., Lo Conte L. and Thornton, J. M. (1999) The CATH Database provides insights into protein structure/function relationships. Nucleic Acids Research, 27, 275-279. [PDF]
Saldanha, J. W., Martin, A. C. R. and Leger, O. J. P. (1999) A single backmutation in the human kIV framework of a previously unsuccessfully humanized antibody restores the binding activity and increases the secretion in cos cells. Molecular Immunology, 36, 709-719. [PDF]
2000
Pearl, F., Todd, A. E., Bray, J. E., Martin, A. C. R., Salamov, A. A., Suwa, M., Swindells, M. B., Thornton, J. M. and Orengo, C. A. (2000) Using the CATH domain database to assign structures and functions to the genome sequences. Biochem. Soc. Trans., 28, 269-275.
Martin, A. C. R. (2000) The Ups and Downs of Protein Topology; Rapid Comparison of Protein Structure, Protein Engineering, 13, 829-837. [PDF]
2002
Martin, A. C. R., Facchiano, A. M., Cuff, A. L., Hernandez-Boussard, T., Olivier, M., Hainaut, P. and Thornton, J. M. (2002) Integrating Mutation Data and Structural Analysis of the p53 Tumour-Suppressor Protein, Human Mutation, 19, 149-164. [PDF]
Allcorn, L. C. and Martin, A. C. R. (2002) SACS - A Self-Maintaining Database of Antibody Crystal Structures, Bioinformatics, 18, 175-181. [PDF]
Kwok, C. H. Y., Au, S. W. N., Martin, A. C. R. and Lam, V. M. S. (2002) G6PDdb: An Integrated Database of Glucose-6-Phosphate Dehydrogenase (G6PD) Mutations, Human Mutation, 19, 217-224. [PDF]
2003
Collis, A. V. J., Brouwer, A. R. and Martin, A. C. R. (2003) Analysis of the Antigen Combining Site - Correlations Between Length and Sequence Composition of the Hypervariable Loops and the Nature of the Antigen J. Mol. Biol., 325, 337-354. [PDF]
Krauss, J., Arndt, M.A.E., Martin, A.C.R., Liu, H. and Rybak, S.M. (2003) Specificity grafting of human antibody frameworks selected from a phage display library: generation of a highly stable humanized anti-CD22 single chain Fv fragment, Protein Engineering, 16,753-759. [PDF]
2004
Harvey, R., Zambon, M., Martin, A. C. R., and Barclay, W.S. (2004) Restrictions to the adaptation of Influenza A Virus H5 haemagglutinin to the Human host, Journal of Virology, 78, 502-507 [PDF]
Martin, A.C.R. (2004) PDBSprotEC: A Web-accessible database linking PDB chains to EC numbers via SwissProt, Bioinformatics, 20, 986-988 Read the article
Cuff, A. L. and Martin, A. C. R. (2004) Analysis of Void Volumes in Proteins and Application to Stability of the p53 Tumour Suppressor Protein J. Mol. Biol., 344, 1199-1209. [PDF]
2005
Cavallo, A. and Martin, A. C. R. (2005) Mapping SNPs to Protein Sequence and Structure Data Bioinformatics, 21, 1443-1450. [PDF preprint] [PDF from OUP]
Martin, Andrew C. R. (2005) Mapping PDB chains to UniProtKB entries, Bioinformatics, 21, 4297-4301 [PDF preprint]. [PDF from OUP]
2006
Fooks, Helen M., Martin, Andrew C. R., Woolfson, Derek N., Sessions, Richard B. and Hutchinson, E. Gail (2006) Amino acid pairing preferences in parallel beta-sheets in proteins, J. Mol. Biol., 356, 32-44
Deevi, S. Vishnu V. and Martin, Andrew C. R. (2006) An extensible automated protein annotation tool: standardizing input and output using validated XML, Bioinformatics, 22,291-296. [PDF] [Free PDF from OUP] [Supplementary information]
Cuff, Alison L., Janes, Robert W. and Martin, Andrew C. R. (2006) Analysing the Ability to Retain Sidechain Hydrogen-bonds in Mutant Proteins, Bioinformatics, 22,1464-1470. [Preprint PDF], [PDF], [Free PDF from OUP] [Supplementary material]
2007
Merelli, E., Armano, G., Cannata, N., Corradini, F., d'Inverno, M., Doms, A., Lord, P., Martin, A., Milanesi, L., Moeller, S., Schroeder, M. and Luck, M. (2007) Agents in Bioinformatics, Computational and Systems Biology, Briefings in Bioinformatics, 8, 45-59 [PDF from BIB][Draft PDF][PDF]
Abhinandan, K. R. and Martin, Andrew C. R. (2007) Analyzing the 'degree of humanness' of antibody sequences, J. Mol. Biol, 369, 852-862. DOI: 10.1016/j.jmb.2007.02.100 [PDF]
Churamani, D., Boulware, M.J., Geach, T.J., Martin, A.C.R., Moy, G.W., Su, Y.-H., Vacquier, V.D., Marchant, J.S., Dale, L. and Patel, S. (2007) Molecular and Functional Characterization of a Novel Intracellular ADP-ribosyl cyclase, PLoS ONE, 2(8), e797. DOI: 10.1371/journal.pone.0000797 [PubMed Central] [PDF Preprint]
2008
Abhinandan, K. R. and Martin, A. C. R. (2008) Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains Molecular Immunology, 45, 3832-3839. [PDF as submitted] [http://dx.doi.org/10.1016/j.molimm.2008.05.022] [PDF]
Reviews, conference proceedings, etc...
1987
Cheetham, J. C., Roberts, S., Martin, A. C. R. amd Rees, A. R. (1987). Molecular Modelling of Antibody Combining Sites. Protein Engineering, 1,232-233. (Meeting Abstract).
1989
Rees, A. R., Martin, A. C. R., Cheetham, J. C. and Webster, D. (1989). Prediction of three-dimensional structure of antibody combining sites. In Proceedings of the Sixth European Seminar and Exhibition on Computer-Aided Molecular Design, 5th-6th October, 1989, (IBC Press). [PDF]
Rees, A. R., Martin, A. C. R., Roberts, S. and Cheetham, J. C. (1989). Combining sites and epitopes defined by molecular modelling, protein engineering and NMR. In Proceedings of the UCLA Symposia on Molecular and Cellular Biology: Protein and Pharmaceutical Engineering, eds. Craik, C., Fletterick, R., Matthews, C. R. and Wells, J., (Liss, New York)
1990
Rees, A. R., Martin, A. C. R., Webster, D. M., Cheetham, J. C., and Roberts, S. (1990). Antibody Combining Sites: Prediction and Design. Biophysical J., 57,A384. (Meeting Abstract).
Gregory, D. St.J., Staunton, D., Martin, A. C. R., Cheetham, J. C., Pedersen, J. T. and Rees, A. R. (1990). Antibody combining sites - Prediction and design, Biochemical Society Symposium, 57, 147-155.
1991
Martin, A. C. R., Cheetham, J. C. and Rees, A. R. (1991). Molecular modelling of antibody combining sites. Methods in Enzymology, 203, 121-153. [PDF]
1994
Martin, A. C. R. (1994) Modelling antibodies: Approach and perspective. Lupus 3, 365-366. [PDF]
1995
Kalsi, J. K., Martin, A. C. R. and Isenberg, D. A. (1995) Structure-function relation of anti-DNA antibodies. Lupus, 4, 245-248. [PDF]
Martin, A. C. R., MacCallum, R. M. and Thornton, J. M. (1995). Analysis and modelling of antibodies. Immunology, 86 Suppl 1, 95. (Meeting Abstract).
2000
Martin, A. C. R. (2000) A practical introduction to the simulation of molecular systems: Book Review, Computers and Chemistry, 24, 239-240. [PDF]
Martin, A. C. R. (2000) Model already exists for fair use of gene data (Correspondence), Nature, 406, 933. [PDF]
2001
Martin, A. C. R. (2001) Modelling Molecular Structures: Book Review, Computers and Chemistry, 25, 309-310. [PDF]
Martin, A. C. R. (2001) Can we integrate bioinformatics data on the internet? (Meeting Report) Trends in Biotechnology 19, 327-328. [PDF]
Corne, D. W. and Martin, A. C. R. (2001) Aritificial Intelligence in Bioinformatics (Editorial) Computers and Chemistry 26, 1-3. Special issue edited by Martin and Corne. [PDF]
Book Chapters...
2001
Martin, A. C. R. (2001) Protein Sequence and Structure Analysis of Antibody Variable Domains. In: Antibody Engineering Lab Manual, ed.: Duebel, S. and Kontermann, R., Springer-Verlag, Heidelberg
2002
Martin, A. C. R. (2002) Comparative Modelling. In: Bioinformatics ed.: Orengo, C. A., Jones, D. T. and Thornton, J. M., Bios Scientific Publishers, Oxford. ISBN 1859960545
Martin, A. C. R. (2002) Internet Technologies for Bioinformatics. In: Bioinformatics ed.: Orengo, C. A., Jones, D. T. and Thornton, J. M. Bios Scientific Publishers, Oxford. ISBN 1859960545
2007
Martin, A. C. R. and Allen, J. (2007) Bioinformatics tools for antibody engineering. In: Handbook of Therapeutic Antibodies Vol 1 (Technologies), ed.: Duebel, S.; Wiley-VCH, Weinheim. ISBN-10: 3-527-31453-9 [Preprint PDF]
Patents...
Rybak, S., Krauss, J., Arndt, M. and Martin, A. C. R. (2003) Specificity grafting of a murine antibody onto a human framework, PCT Application PCT/US03/1933; WO 03105782. (Priority date 17 June 2002).
Martin, A. C. R. (2000) Process for storing data, PCT Application PCT/GB01/01123; WO 2001/069413, WO0169413; US2004030502 (Priority date 14 March 2000).
Lost but not forgotten...
Papers that were submitted/accepted, but for which I have no reference...
Jones, S., Martin, A. C. R., Karmirantzou, M., Laskowski, R. A., Orengo, C. and Thornton, J. M. Protein Domains, Folds and Functions, Transactions, American Crystallography Association Annual Meeting 1997
In press...
Hurst, J. M., McMillan, L. E. M., Porter, C. T., Allen, J. Fakorede, A. and Martin, A. C. R. (2008) The SAAPdb web resource: a large scale structural analysis of mutant proteins, Human Mutation, in press. [PDF as submitted]
Submitted papers...
McMillan, L. E. M. and Martin, A. C. R. (2008) Automatically extracting functionally equivalent proteins from SwissProt, Submitted to BMC Bioinformatics.
