Publications

Refereed...

1989 .. 1992 .. 1993 .. 1995 .. 1996 .. 1997 .. 1998 .. 1999 .. 2000 .. 2002 .. 2003 .. 2004 .. 2005 .. 2006 .. 2007 .. 2008 .. 2009 .. 2010 .. 2011 .. 2012 .. 2013 .. In Press

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, A.C.R. (2005) Mapping PDB chains to UniProtKB entries, Bioinformatics, 21, 4297-4301 [PDF preprint]. [PDF from OUP]

2006

Fooks, H.M., Martin, A.C.R., Woolfson, D.N., Sessions, R.B. and Hutchinson, E.G. (2006) Amino acid pairing preferences in parallel beta-sheets in proteins, J. Mol. Biol., 356, 32-44 [PDF]

Deevi, S.V.V. and Martin, A.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, A.L., Janes, R.W. and Martin, A.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, A.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] [Supplementary material]

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]

McMillan, L.E.M. and Martin, A.C.R. (2008) Automatically extracting functionally equivalent proteins from SwissProt, BMC Bioinformatics, 9, 418. [Article online] [Free PDF]

Churamani, D., Boulware, M., Ramakrishnan, L., Geach, T., Martin, A.C.R., Vacquier, V., Marchant, J., Dale, L. and Patel, S. (2008) Molecular characterisation of a novel cell surface ADP-ribosyl cyclase from the sea urchin, Cellular Signalling, 20, 2347-2355. [PDF]

2009

Hurst, J.M., McMillan, L.E.M., Porter, C.T., Allen, J. Fakorede, A. and Martin, A.C.R. (2009) The SAAPdb web resource: a large scale structural analysis of mutant proteins, Human Mutation, 30, 616-624. [PDF as submitted] [PDF] [Supporting Materials]

Izarzugaza, J.M.G., Baresic, A., McMillan, L.E.M., Yeats, C., Clegg, A., Orengo, C.A., Martin, A.C.R. and Valencia, A. (2009) An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D BMC Bioinformatics. 10 Suppl 8, S5-S5. [Free PDF] [Web server]

2010

cover image

Baresic, A., McMillan, L.E.M., Rogers, H.H., Hurst, J.M. and Martin, A.C.R (2010) Compensated pathogenic deviations: analysis of structural effects, Journal of Molecular Biology, 396, 19-30. DOI: http://dx.doi.org/10.1016/j.jmb.2009.11.002 [PDF as submitted] [PDF] [Supporting Material]

Thullier, P., Huish, O., Pelat, T. and Martin, A.C.R. (2010) The humanness of macaque antibody sequences, Journal of Molecular Biology, 396, 1439-1450. DOI: http://dx.doi.org/10.1016/j.jmb.2009.12.041 [PDF as submitted] [PDF]

Hirtreiter, A., Damska, G.E., Cheung, A., Klose, D., Grohmann, D., Vojnic, E., Martin, A.C.R., Cramer, P. and Werner, F. (2010) Spt4/5 Stimulates Transcription Elongation Through The RNA Polymerase Clamp Coiled Coil Motif Nucleic Acids Research, 38, 4040-4051 doi:10.1093/nar/gkq135 [PDF]

Abhinandan, K.R. and Martin, A.C.R. (2010) Analysis and Prediction of VH/VL Packing in Antibodies Protein Engineering Design and Selection, 23, 689-697. doi:10.1093/protein/gzq043 [PDF as submitted] [PDF from OUP] [PDF]

2011

Nan, R., Farabella, I., Schumacher, F.F., Miller, A., Gor, J., Martin, A.C.R., Jones, D.T., Lengyel, I. and Perkins, S.J. (2011) Zinc binding to the Tyr402 and His402 allotypes of complement factor H: possible implications for age-related macular degeneration, J. Mol. Biol. 408,714-735. [PDF As Submitted] [PDF]

Izarzugaza, J.M.G., Hopcroft, L.E.M., Baresic, A., Orengo, C.A., Martin, A.C.R. and Valencia, A. (2011) Characterizing Pathogenic Germline Deviations in Human Protein Kinases. BMC Bioinformatics (special issue - Proceedings of the European Conference on Computational Biology (ECCB) 2010 Workshop: Annotation, interpretation and management of mutation (AIMM)) 12 Suppl.4, S1. [Free PDF from BMC],[Free PDF][Supplementary Material]

2012

Jayaram, N., Bhowmick, P. and Martin, A.C.R. (2012) Germline VH/VL Pairing in Antibodies, Protein Engineering Design and Selection 25, 523-530 doi:10.1093/protein/gzs043 [PDF As Submitted] [Free PDF from OUP] [PDF][Supplementary Material]

Usifo, E., Leigh, S.E.A., Whittall, R.A., Lench, N., Taylor, A., Yeats, C., Orengo, C.A., Martin, A.C.R., Celli, J. and Humphries, S.E. (2012) Low Density Lipoprotein Receptor Gene Familial Hypercholesterolemia Variant Database: update and pathological assessment, Annals of Human Genetics, 76, 387-401. DOI: 10.1111/j.1469-1809.2012.00724.x [PDF]

2013

Osborne, T., Heath, M., Martin, A.C.R., Pankowski, J., Hudson-Edwards, K., and Santini, J. (2013) Cold-adapted arsenite oxidase from a psychrotolerant Polaromonas species, Metallomics, 5, 318-324. DOI: 10.1039/c2mt20180a [PDF]

Al-Numair, N.S. and Martin, A.C.R. (2013) The SAAP pipeline and database: tools to analyze the impact and predict the pathogenicity of mutations, BMC Genomics, (ISMB 2012 SNP-SIG Special Issue) 14(Suppl 3):S4 [Free from BMC Genomics] [Free PDF]

In Press

Martin, A.C.R. (in press) Structural Biology of Moonlighting - Lessons from Antibodies, Biochem Soc Trans [PDF as submitted]


Reviews, conference proceedings, etc...

1987 .. 1989 .. 1990 .. 1991 .. 1994 .. 1995 .. 2000 .. 2001 .. 2010 .. 2011 2013

1987

Cheetham, J.C., Roberts, S., Martin, A.C.R. and 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, Thirty-Fourth Annual Meeting of the Biophysical Society, February 18-22, 1990 Baltimore Convention Center Baltimore, Maryland ). [Free PDF]

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]

2010

Izarzugaza, J.M.G., McMillan, L.E.M., Baresic, A., Orengo, C.A., Martin, A.C.R. and Valencia, A. (2010) Characterizing Pathogenic Germline Deviations in Human Protein Kinases in Proceedings of the Workshop on Annotation, Interpretation and Management of Mutations (AIMM-2010); a workshop at ECCB10. Ghent, Belgium, September 26th, 2010. Ed. Christopher J.O. Baker, Rene Witte, Dietrich Rebholz-Schuhmann. [Free PDF from AIMM2010] [Free PDF]

2011

Baresic, A. and Martin, A.C.R. (2011) Compensated Pathogenic Mutations, Biomolecular Concepts 2,281-292. DOI: 10.1515/BMC.2011.025 [PDF from Biomolecular Concepts][PDF][PDF As Submitted]

Henderson, B. and Martin, A.C.R. (2011) Bacterial Virulence in the Moonlight: Multitasking Bacterial Moonlighting Proteins are Virulence Determinants in Infectious Disease, Infection and Immunity, 79, 3476-91. DOI:10.1128/IAI.00179-11[PDF As Submitted], [PDF]

2013

Henderson, B. and Martin, A.C.R. (2013) Bacterial Moonlighting Proteins and Bacterial Virulence, Current Topics in Microbiology and Immunology, 358, 155-213. [PDF As Submitted], DOI: 10.1007/82_2011_188


Book Chapters...

2001 .. 2002 .. 2007 .. 2010

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]

2010

Martin, A.C.R. (2010) Protein Sequence and Structure Analysis of Antibody Variable Domains. In: Antibody Engineering Lab Manual Volume 2 (2nd Edition), ed.: Duebel, S. and Kontermann, R., Springer-Verlag, Heidelberg. ISBN-10: 3642011462, ISBM-13: 978-3642011467 [Free PDF]

2013

Martin, A.C.R. and Allen, J. (2013) Bioinformatics tools for antibody engineering. In: Handbook of Therapeutic Antibodies Vol 1 (Technologies) - 2nd Edition, ed.: Duebel, S.; Wiley-VCH, Weinheim. [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, US Patent 7,456,260 (Issued 25 Nov 2008) Applications: 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


Submitted papers...

Martin, A.C.R. (2014) Structural Biology of Moonlighting - Lessons from Antibodies, Submitted to Procedings of the Biochemical Society [PDF As Submitted]

Martin, A.C.R. (2014) JSAV: JavaScript Sequence Alignment Viewer (Application Note), Submitted to F1000 Research [PDF As Submitted]

Jayaram, N., Usvyat, D. and Martin, A.C.R. (2014) Optimizing the Prediction of Transcription Factor Binding Sites, Submitted to Bioinformatics [PDF As Submitted]