Articles
2025
Sweet-Jones, J. and Martin, A.C.R. (2025) An antibody developability triaging pipeline exploiting protein language models. mAbs 17:2472009. [Supplementary Material (1)] [Supplementary Material (2)] [Supplementary Material (3)] [doi:10.1080/19420862.2025.2472009] [Free PDF] [PDF from publisher] [PDF as submitted].
2024
Lin, W., Wells, J., Wang, Z., Orengo, C. and Martin, A.C.R. (2024) Enhancing missense variant pathogenicity prediction with protein language models using VariPred. Scientific Reports 14:8136. [doi:10.1038/s41598-024-51489-7] [Free PDF].
Liu, C., Denzler, L.M.A., Hood, O.E.C. and Martin, A.C.R. (2024) Do antibody CDR loops change conformation upon binding?. mAbs 16:2322533. [doi:10.1080/19420862.2024.2322533] [Free PDF] [PDF as submitted].
Liu, C., Denzler, L.M.A, Chen, Y., Martin, A.C.R. and Paige, B. (2024) AsEP: benchmarking deep learning methods for antibody-specific epitope prediction. arXiv Machine Learning (cs.LG):arXiv:2407.18184v2. [Supplementary Material] [doi:10.48550/arXiv.2407.18184] [Free PDF].
2023
Boron, V.A. and Martin, A.C.R. (2023) abYpap: improvements to the prediction of antibody VH/VL packing using gradient boosted regression. Protein Engineering Design and Selection 36:1-8. [doi:10.1093/protein/gzad021] [PDF as submitted].
2022
Guimaraes Koch, S.S., Thorpe, R., Kawasaki, N., Lefranc, M.-P., Malan, S., Martin, A.C.R., Mignot, G., Pluckthun, A., Rizzi, M., Shubat, S., Weisser, K. and Balocco, R. (2022) International Nonproprietary Names (INN) for monoclonal antibodies: an evolving nomenclature system. mAbs 14:e2075078. [doi:10.1080/19420862.2022.2075078] [Free PDF] [PDF as submitted].
Sweet-Jones, J., Ahmad, M. and Martin, A.C.R. (2022) Antibody markup language (AbML) - a notation language for antibody-based drug formats and software for creating and rendering AbML (abYdraw). mAbs 14:e2101183. [doi:10.1080/19420862.2022.2101183] [PDF as submitted].
2021
Ireland, S.M. and Martin, A.C.R. (2021) ZincBindPredict - prediction of zinc binding sites in proteins. Molecules 26:966. [Web server] [Supplementary Material] [doi:10.3390/molecules26040966] [Free PDF] [PDF from publisher].
Ireland, S.M. and Martin, A.C.R. (2021) GraphQL for the delivery of bioinformatics web APIs and application to ZincBind. Bioinformatics Advances Pages: vbab023. [Web server] [doi:10.1093/bioadv/vbab023] [PDF] [PDF from publisher] [PDF as submitted].
2020
Ireland, S.M. and Martin, A.C.R. (2020) atomium - a Python structure parser. Bioinformatics 36:2750-2754. [Supplementary Material] [doi:10.1093/bioinformatics/btaa072] [PDF from publisher] [PDF as submitted].
2019
Ireland, S.M. and Martin, A.C.R. (2019) ZincBind - the database of zinc binding sites. Database. [Web server] [doi:10.1093/database/baz006] [Free PDF] [PDF from publisher] [PDF as submitted].
Ferdous, S., Kelm, S., Baker, T.S., Shi, J. and Martin, A.C.R. (2019) B-cell epitopes: Discontinuity and conformational analysis. Molecular Immunology 114:643-650. [Supplementary Material] [doi:10.1016/j.molimm.2019.09.014] [PDF as submitted].
2018
Ferdous, S. and Martin, A.C.R. (2018) AbDb: antibody structure database - a database of PDB derived antibody structures. Database 2018:bay040. [doi:10.1093/database/bay040] [PDF] [PDF from publisher] [PDF as submitted].
2017
Swindells, M.B., Porter, C.T., Couch, M., Hurst, J., Abhinandan, K.R., Nielsen, J.H., Macindoe, G., Hetherington, J. and Martin, A.C.R. (2017) abYsis: integrated antibody sequence and structure - management, analysis and prediction. Journal of Molecular Biology 429:356-364. [PMID: 27561707] [PDF] [PDF as submitted].
Northey, T., Baresic, A. and Martin, A.C.R. (2017) IntPred: a structure-based predictor of protein-protein interaction sites. Bioinformatics 34:223-229. [Supplementary Material] [doi:10.1093/bioinformatics/btx585] [PMID: 28968673] [PDF from publisher] [PDF as submitted].
2016
Martin, A.C.R. and Rees, A.R. (2016) Extracting human antibody sequences from public databases for antibody humanization: high frequency of species assignment errors. Protein Engineering Design and Selection 29:403-408. [Supplementary Material] [PMID: 27274090] [PDF] [PDF from publisher] [PDF as submitted].
Al-Numair, N.S., Lopes, L., Syrris, P., Monserrat, L., Elliott, P. and Martin, A.C.R. (2016) The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants. Bioinformatics 32:2947-2955. [Supplementary Material] [doi:10.1093/bioinformatics/btw362] [PMID: 27318203] [PDF] [PDF as submitted].
Jayaram, N., Usvyat, D. and Martin, A.C.R. (2016) Evaluating tools for transcription factor binding site prediction. BMC Bioinformatics. [Supplementary Material] [doi:10.1186/s12859-016-1298-9] [PMID: 27806697] [PDF from publisher] [PDF as submitted].
2015
Porter, C.T. and Martin, A.C.R. (2015) BiopLib and BiopTools - a C programming library and toolset for manipulating protein structure (application note). Bioinformatics 31:4017-4019. [PMID: 26323716] [Free PDF] [PDF from publisher] [PDF as submitted].
2014
Martin, A.C.R. (2014) Viewing multiple sequence alignments with the Javascript sequence alignment viewer (JSAV). F1000Research 3:249. [doi:10.12688/f1000research.5486.1] [PMID: 25653836] [Free PDF] [PDF from publisher].
Martin, A.C.R. (2014) Structural biology of moonlighting - lessons from antibodies. Biochem Soc Trans 42:1704-1708. [PMID: 25399593] [PDF] [PDF from publisher] [PDF as submitted].
Henderson, B. and Martin, A.C.R. (2014) Protein moonlighting: a new factor in biology and medicine. Biochem. Soc. Trans. 42:1671-1678. [PMID: 25399588] [PDF] [PDF from publisher].
Leigh, S.E.A., Lee, Y.P., Whittall, R.A., Dawson, N., Das, S., Martin, A.C.R., Orengo, C.A. and Humphries, S.E. (2014) Update and analysis of the UCL pro-protein convertase subtilisin/kexin type9 gene (PCSK9) variant database. Atherosclerosis 235:E98. [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] [PMID: 23150098] [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. [PMID: 20591902] [Free PDF] [PDF from publisher].
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. [Supplementary Material] [doi:10.1093/protein/gzs043] [PMID: 22802295] [PDF] [PDF from publisher] [PDF as submitted].
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] [PMID: 22881376] [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. [PMID: 21396937] [Free PDF] [PDF as submitted].
Izarzugaza, J.M.G., Hopcroft, L.E.M., Baresic, A., Orengo, C.A., Martin, A.C.R. and Valencia, A. (2011) Characterization of pathogenic germline deviations in human protein kinases. BMC Bioinformatics 12 Suppl.4:S1. Special Issue - Proceedings of the European Conference on Computational Biology (ECCB) 2010 Workshop: Annotation, interpretation and management of mutation (AIMM-2010) [Supplementary Material] [PMID: 21992016] [Free PDF] [PDF from publisher] [PDF as submitted].
2010
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. [Supplementary Material] [doi:10.1016/j.jmb.2009.11.002] [PMID: 19900462] [PDF] [PDF as submitted].
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:10.1016/j.jmb.2009.12.041] [PMID: 20043919] [PDF] [PDF as submitted].
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] [PMID: 20197319] [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] [PMID: 20591902] [PDF] [PDF from publisher] [PDF as submitted].
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. [Supplementary Material] [PMID: 19191322] [PDF] [PDF as submitted].
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. [Web server] [PMID: 19758469] [Free PDF].
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. [doi:10.1016/j.molimm.2008.05.022] [PMID: 18614234] [PDF] [PDF as submitted].
McMillan, L.E.M. and Martin, A.C.R. (2008) Automatically extracting functionally equivalent proteins from SwissProt. BMC Bioinformatics 9:418. [PMID: 18838004] [Free PDF] [PDF from publisher].
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. [PMID: 18824228] [PDF].
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. [PMID: 16772270] [PDF] [PDF from publisher] [PDF as submitted].
Abhinandan, K.R. and Martin, A.C.R. (2007) Analyzing the 'degree of humanness' of antibody sequences. J. Mol. Biol 369:852-862. [Supplementary Material] [doi:10.1016/j.jmb.2007.02.100] [PMID: 17442342] [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] [PMID: 17726527] [PDF from publisher] [PDF as submitted].
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. [Web server] [PMID: 16337654] [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. [Web server] [doi:10.1093/bioinformatics/bti808] [PMID: 16339285] [PDF] [PDF from publisher].
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. [Web server] [PMID: 16601005] [PDF] [PDF from publisher] [PDF as submitted].
2005
Cavallo, A. and Martin, A.C.R. (2005) Mapping SNPs to protein sequence and structure data. Bioinformatics 21:1443-1450. [PMID: 15613399] [PDF from publisher] [PDF as submitted].
Martin, A.C.R. (2005) Mapping PDB chains to UniProtKB entries. Bioinformatics 21:4297-4301. [PMID: 16188924] [PDF] [PDF from publisher] [PDF as submitted].
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. [PMID: 14671130] [PDF].
Martin, A.C.R. (2004) PDBSprotEC: a web-accessible database linking PDB chains to EC numbers via SwissProt. Bioinformatics 20:986-988. [PMID: 14764547] [Free PDF] [PDF from publisher].
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. [PMID: 15561139] [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. [PMID: 12488099] [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. [PMID: 14600205] [PDF].
2002
Martin, A.C.R., Facchiano, A.M., Cuff, A.L., Hernandez-Boussard, T., Olivier, M., Hainaut, P. and Thornton, J.M. (2002) Mutation data and structural analysis of the p53 tumour-suppressor protein. Human Mutation 19:149-164. [PMID: 11793474] [Free PDF].
Allcorn, L.C. and Martin, A.C.R. (2002) SACS - a self-maintaining database of antibody crystal structures. Bioinformatics 18:175-181. [PMID: 11836226] [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. [PMID: 11857737] [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. [PMID: 10816141] [PDF] [PDF from publisher].
Martin, A.C.R. (2000) Ups and downs of protein topology; rapid comparison of protein structure. Protein Engineering 13:829-837. [PMID: 11239082] [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. [PMID: 10398401] [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. [PMID: 9847200] [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. [PMID: 10593510] [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. [PMID: 9485213] [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. [Web server] [PMID: 9687369] [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. [PMID: 9749368] [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. [PMID: 10089492] [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. [PMID: 9194170] [PDF].
Martin, A.C.R., MacArthur, M.W. and Thornton, J.M. (1997) Assessment of comparative modelling in CASP2. PROTEINS: Structure, Function and Genetics 29, Suppl. 1:14-28. [PMID: 9485491] [PDF].
Jones, S., Martin, A.C.R., Karmirantzou, M., Laskowski, R.A., Orengo, C. and Thornton, J.M. (1997). Protein domains, folds and functions. In Transactions of the american crystallography association Eds. Gilliland, G. and Berman, H. Volume: 32, 'Structural Informatics' (American Crystollographic Association).
1996
Martin, A.C.R. (1996) Accessing the Kabat antibody sequence database by computer. PROTEINS: Structure, Function and Genetics 25:130-133. [PMID: 8727325] [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. [PMID: 8676898] [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. [PMID: 8876650] [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. [PMID: 8947577] [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. [PMID: 7567924] [PDF].
Martin, A.C.R., Toda, K., Stirk, H.J. and Thornton, J.M. (1995) Long loops in proteins. Protein Engineering 8:1093-1101. [PMID: 8819975] [PDF].
1993
Martin, A.C.R. (1993) MoG: molecular graphics for the Commodore Amiga. Journal of Molecular Graphics 11:53-55. [PMID: 8499396] [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. [PMID: 8433968] [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. [PMID: 1409555] [PDF].
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. [PMID: 1762554] [PDF].
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. [PMID: 2594766] [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. Pages: 35-54 (Liss, New York). ISBN: 047156771X, 9780471567714.
Reviews
2022
Khetan, R., Curtis, R., Deane, C.M., Hadsund, J.T., Kar, U., Krawczyk, K., Kuroda, D., Robinson, S.A., Sormanni, P., Tsumoto, K., Warwicker, J. and Martin, A.C.R. (2022) Current advances in biopharmaceutical informatics: guidelines, impact and challenges in computational developability assessment of antibody therapeutics (Review). mAbs 14:e2020082. [doi:10.1080/19420862.2021.2020082] [Free PDF] [PDF from publisher].
2013
Henderson, B. and Martin, A.C.R. (2013) Bacterial moonlighting proteins and bacterial virulence (Review). Current Topics in Microbiology and Immunology 358:155-213. [doi:10.1007/82_2011_188] [PMID: 22143554] [PDF as submitted].
2011
Baresic, A. and Martin, A.C.R. (2011) Compensated pathogenic mutations (Review). Biomolecular Concepts 2:281-292. [doi:10.1515/BMC.2011.025] [PMID: 25962036] [PDF] [PDF from publisher] [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 (Review). Infection and Immunity 79:3476-91. [doi:10.1128/IAI.00179-11] [PMID: 21646455] [PDF] [PDF as submitted].
1995
Kalsi, J.K., Martin, A.C.R. and Isenberg, D.A. (1995) Structure-function relation of anti-DNA antibodies (Review). Lupus 4:245-248. [PMID: 8528217] [PDF].
1994
Martin, A.C.R. (1994) Modelling antibodies: approach and perspective (Review). Lupus 3:365-366. [PMID: 7841988] [PDF].
1990
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 (Review). Biochemical Society Symposium 57:147-155. [PMID: 2099739].
Book chapters
2018
Martin, A.C.R., Baresic, A. and Al-Numair, N. (2018). Structural impact of single nucleotide variations (SNVs) (Book chapter). In Encyclopedia of biophysics (2nd edition) Eds. Roberts, G.K. and Watts, A. (Springer-Verlag, Berlin Heidelberg). ISBN 978-3-642-16711-9 [doi:10.1007/978-3-642-35943-9_430-1] [PDF] [PDF as submitted].
2017
Martin, A.C.R. (2017). An introduction to the protein molecule (Book chapter). In Protein moonlighting in biology and medicine, the biological and biomedical consequences of protein moonlighting Eds. Henderson, B., Fares, M.A. and Martin, A.C.R. (Wiley-Blackwell, Hoboken, New Jersey). Chapter 1. ISBN-10: 1118952081; ISBN-13: 978-1118952085 [PDF as submitted].
Martin, A.C.R. (2017). The structural basis of protein moonlighting (Book chapter). In Protein moonlighting in biology and medicine, the biological and biomedical consequences of protein moonlighting Eds. Henderson, B., Fares, M.A. and Martin, A.C.R. (Wiley-Blackwell, Hoboken, New Jersey). Chapter 4. ISBN-10: 1118952081; ISBN-13: 978-1118952085 [PDF as submitted].
2014
Martin, A.C.R. and Allen, J. (2014). Bioinformatics tools for antibody engineering (Book chapter). In Handbook of therapeutic antibodies vol 1, Technologies (2nd edition) Eds. Duebel, S. and Reichert, J. (Wiley-Blackwell, Weinheim). ISBN-10: 3527329374, ISBN-13: 978-3527329373 [PDF as submitted].
2013
Martin, A.C.R. and Baresic, A. (2013). Structural impact of SNPs (Book chapter). In Encyclopedia of biophysics Ed. Roberts, G.K. (Springer-Verlag, Berlin Heidelberg). ISBN 978-3-642-16711-9. [PDF as submitted].
2010
Martin, A.C.R. (2010). Protein sequence and structure analysis of antibody variable domains (Book chapter). In Antibody engineering lab manual volume 2 (2nd edition) Eds. Duebel, S. and Kontermann, R. (Springer-Verlag, Heidelberg). ISBN-10: 3642011462, ISBN-13: 978-3642011467 [PDF as submitted].
2007
Martin, A.C.R. and Allen, J. (2007). Bioinformatics tools for antibody engineering (Book chapter). In Handbook of therapeutic antibodies vol 1, Technologies Ed. Duebel, S. (Wiley-VCH, Weinheim). ISBN-10: 3-527-31453-9 [PDF as submitted].
2002
Martin, A.C.R. (2002). Comparative modelling (Book chapter). In Bioinformatics Eds. 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 (Book chapter). In Bioinformatics Eds. Orengo, C.A., Jones, D.T. and Thornton, J.M. (Bios Scientific Publishers, Oxford). ISBN: 1859960545.
2001
Martin, A.C.R. (2001). Protein sequence and structure analysis of antibody variable domains (Book chapter). In Antibody engineering lab manual Eds. Duebel, S. and Kontermann, R. (Springer-Verlag, Heidelberg).
Meeting Abstracts
2024
Liu, C., Denzler, L. M. A., Chen, Y., Paige, B. and Martin, A. C. R. (2024) AsEP: benchmarking deep learning methods for antibody-specific epitope prediction (Meeting abstract). Conference on Neural Information Processing Systems (NeurIPS), Vancouver Convention Center. [Supplementary Material] [doi:10.5281/zenodo.11495514].
2007
Martin, Andrew, Tyson, Kerry, Page, Matt, Fossati, Gianluca , Snowden, James, Abhinandan, Raghavan, Lawson, Alastair, Nesbitt, Andrew and Popplewell, Andrew (2007) Comparison of naturally occurring human immunoglobulin sequences with the anti-tnf agents certolizumab pegol, adalimumab, and infliximab (Meeting abstract). Clinical Immunology Volume: 123 Supp-S. [doi:10.1016/j.clim.2007.03.127] [Free PDF].
2006
Arndt, Michaela, Vu, Bang K., Martin, Andrew C.R., Liu, Huaitian, Newton, Dianne L., Seeber, Siegfried, Rybak, Susanna M. and Krauss, Jurgen (2006) A humanized diabody-ribonuclease fusion protein mediates potent and selective killing of CD22-positive tumor cells (Meeting abstract). Journal of Immunotherapy 29:671. [doi:10.1097/01.cji.0000211343.73588.59] [PDF] [PDF from publisher].
1995
Martin, A.C.R., MacCallum, R.M. and Thornton, J.M. (1995) Analysis and modelling of antibodies (Meeting abstract). Immunology 86 Suppl 1:95.
1990
Rees, A.R., Martin, A.C.R., Webster, D.M., Cheetham, J.C., and Roberts, S. (1990) Antibody combining sites: prediction and design (Meeting abstract). Biophysical J 57:A384. (Thirty-Fourth Annual Meeting of the Biophysical Society, February 18-22, 1990 Baltimore Convention Center Baltimore, Maryland) [Free PDF].
1989
Rees, A.R., Martin, A.C.R., Cheetham, J.C. and Webster, D. (1989) Prediction of three-dimensional structure of antibody combining sites (Meeting abstract). Proceedings of the Sixth European Seminar and Exhibition on Computer-Aided Molecular Design 5th-6th October, 1989, (IBC Press). [PDF].
1987
Cheetham, J.C., Roberts, S., Martin, A.C.R. and Rees, A.R. (1987) Molecular modelling of antibody combining sites (Meeting abstract). Protein Engineering 1:232-233. [PDF].
Other
2019
Martin, A.C.R. (2019) Cyrus Chothia - in memorium (Obituary). Obituary for the Antibody Society.
2018
Martin, A.C.R. (2018) Recommendation: Changes to the International Nonproprietary Names for antibody therapeutics 2017 and beyond: of mice, men and more (Parren, P.W.H.I, Carter, P.J. and Pluckthun, A.) (F1000 recommendation). [PDF].
Martin, A.C.R. (2018) Recommendataion: The H3 loop of antibodies shows unique structural characteristics (F1000 recommendation). [PDF].
2017
Martin, A.C.R. (2017) Anna Tramontano - in memorium (Obituary). Obituary for the Antibody Society.
Martin, A.C.R. (2017) Recommendation: Improving B-cell epitope prediction and its application to global antibody-antigen docking (Krawczyk K, Liu X, Baker T, Shi J, Deane C.M.) (F1000 recommendation). [PDF].
Martin, A.C.R. (2017) Recommendation: Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint (Weitzner B.D., Gray J.J.) (F1000 recommendation). [PDF].
2016
Ferdous, S. and Martin, A.C.R. (2016) Exploration of conformational B-cell epitopes: components to peptide-based vaccines (ECCB) (Poster). F1000Research 5:2142. [doi:10.7490/f1000research.1112977.1] [PDF as submitted].
2015
Ferdous, S. and Martin, A.C.R. (2015) Characterization and structural analysis of B-cell epitopes for vaccine and therapeutic antibody design (ISMB) (Poster). F1000Research 4:523. [doi:10.7490/f1000research.1110268.1] [PDF as submitted].
2005
Armano, G., Denzinger, J., Martin, A., Merelli, E., Miles, S., Tianfield, H. and Unland, R. (2005) First international workshop on multi-agent systems for medicine, computational biology, and bioinformatics (Editorial). Proceedings of the Fourth International Joint Conference on Autonomous Agents and Multi-agent Systems (AAMAS '05) 2005:preface. Workshop co-organizer [PDF] [PDF from publisher].
2003
Rybak, S., Krauss, J., Arndt, M. and Martin, A.C.R. (2003) Specificity grafting of a murine antibody onto a human framework (Patent). US Patent 7,456,260. Issued 25 Nov 2008. (Priority date 17 June 2002). PCT/US03/1933 WO03105782.
Rybak, S., Krauss, J., Arndt, M. and Martin, A.C.R. (2003) Specificity grafting of a murine antibody onto a human framework (Patent). EU Patent EP1551453 equivalent of US7,456,260. [PCT].
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].
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].
Martin, A.C.R. (2000) Process for storing data (Patent). US Patent US2004030502 application priority date 14 March 2000. PCT/GB01/01123; WO2001/069413; WO0169413.
1999
Ravirajan, C.T., Rahman, M.A., Papadaki, L., Griffiths, M.H., Kalsi, J., Martin, A.C.R., Ehrenstein, M.R., Latchman, D.S. and Isenberg, D.A. (1999) Correction: genetic, structural and functional properties of an IgG DNA-binding monoclonal antibody from a lupus patient with nephritis (European Journal of Immunology 28(1998)339-350) (Correction). European Journal of Immunology 29:3052.