@article{martin:camal, author="Martin, A.C.R. and Cheetham, J.C. and Rees, A.R.", year=1989, pmid="2594766", title="Modelling antibody hypervariable loops: A combined algorithm", journal="Proceedings of the National Academy of Science", volume="86", pages="9269-9272", pdf="pdf/pnas.pdf" } @article{jackson:antitest, author="Jackson, T. and Morris, B.A. and Martin, A.C.R. and Lewis, D.F.V. and Sanders, P.G.", year=1992, pmid="1409555", title="Molecular modelling and site-directed mutagenesis on a bovine anti-testosterone monoclonal antibody", journal="Protein Engineering", volume="5", pages="343-350", pdf="pdf/jackson.pdf" } @article{martin:mog, author="Martin, A.C.R.", year=1993, pmid="8499396", title="{MoG}: Molecular graphics for the {Commodore Amiga}", journal="Journal of Molecular Graphics", volume="11", pages="53-55", pdf="pdf/mog.pdf" } @article{gregory:conrad, author="Gregory, D.St.J. and Martin, A.C.R. and Cheetham, J.C. and Rees, A.R.", year=1993, pmid="8433968", title="The prediction and characterization of metal binding sites in proteins", journal="Protein Engineering", volume="6", pages="29-35", pdf="pdf/gregory.pdf" } @article{reczko:tdnn, author="Reczko, M. and Martin, A.C.R. and Bohr, H. and Suhai, S.", year=1995, pmid="7567924", title="Prediction of hypervariable {CDR-H3} loop structures in antibodies", journal="Protein Engineering", volume="8", pages="389-395", pdf="pdf/reczko.pdf" } @article{martin:longloops, author="Martin, A.C.R. and Toda, K. and Stirk, H.J. and Thornton, J.M.", year=1995, pmid="8819975", title="Long loops in proteins", journal="Protein Engineering", volume="8", pages="1093-1101", pdf="pdf/longloops.pdf" } @article{martin:kabatman, author="Martin, A.C.R.", year=1996, pmid="8727325", title="Accessing the {Kabat} antibody sequence database by computer", journal="PROTEINS: Structure, Function and Genetics", volume="25", pages="130-133", pdf="pdf/kabatman.pdf" } @article{kalsi:modantidna, author="Kalsi, J.K. and Martin, A.C.R. and Hirabayashi, Y. and Ehrenstein, M. and Longhurst, C.M. and Ravirajan, C. and Zvelebil, M. and Stollar, D. and Thornton, J.M. and Isenberg, D.A.", year=1996, pmid="8676898", title="Functional and modelling studies of the binding of Human monoclonal anti-{DNA} antibodies to {DNA}", journal="Molecular Immunology", volume="33", pages="471-483", pdf="pdf/funcmod.pdf" } @article{maccallum:bindingsites, author="MacCallum, R.M. and Martin, A.C.R. and Thornton, J.M.", year=1996, pmid="8876650", title="Antibody-antigen interactions: Contact analysis and binding site topography", journal="J. Mol. Biol", volume="262", pages="732-745", pdf="pdf/maccallum.pdf" } @article{martin:canonicals, author="Martin, A.C.R. and Thornton, J.M.", year=1996, pmid="8947577", title="Structural families of loops in homologous proteins: Automatic classification, modelling and application to antibodies", journal="J.Mol.Biol", volume="263", pages="800-815", pdf="pdf/strucfamilies.pdf" } @article{kibryanov:anticd3, author="Kipriyanov, S.M. and Moldenhauer, G. and Martin, A.C.R. and Kupriyanova, O.A. and Little, M.", year=1997, pmid="9194170", title="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", journal="Protein Engineering", volume="10", pages="445-453", pdf="pdf/kipryanov.pdf" } @article{martin:casp2, author="Martin, A.C.R. and MacArthur, M.W. and Thornton, J.M.", year=1997, pmid="9485491", title="Assessment of Comparative Modelling in {CASP2}", journal="PROTEINS: Structure, Function and Genetics", volume="29, Suppl.~1", pages="14-28", pdf="pdf/casp2.pdf" } @article{ravirajan:antidna, author="Ravirajan, C.T. and Rahman, M.A. and Papadaki, L. and Griffiths, M. and Kalsi, J. and Martin, A.C.R. and Ehrenstein, M.R. and Latchman, D.S. and Isenberg, D.A.", year=1998, pmid="9485213", title="Genetic Structural and Functional Properties of a Human {IgG} Anti-{DNA} Antibody", journal="European Journal of Immunology", volume="28", pages="339-350", pdf="pdf/ravirajan.pdf" } @article{martin:foldsandfunctions, author="Martin, A.C.R. and Orengo, C.A. and Hutchinson, E.G. and Jones, S. and Karmirantzou, M. and Laskowski, R.A. and Mitchell, J.B.O. and Taroni, C. and Thornton, J.M.", year=1998, pmid="9687369", title="Protein Folds and Functions", journal="Structure", volume="6", pages="875-884", web="/cathwheel/", pdf="pdf/foldsandfunctions.pdf" } @article{zuccotto:dhfr, author="Zuccotto, F. and Martin, A.C.R. and Laskowski, R.A. and Gilbert, I. and Thornton, J.M.", year=1998, pmid="9749368", title="Dihydrofolate Reductase: a Potential Drug Target in Trypanosomes and {Leishmania}", journal="Journal of Computer Aided Molecular Design", volume="12", pages="241-257", pdf="pdf/zuccotto.pdf" } @article{orengo:classifying, author="Orengo, C.A. and Martin, A.C.R. and Hutchinson, G. and Jones, S. and Jones. D.J. and Michie, A.D. and Swindells, M.B. and Thornton, J.M.", year=1998, pmid="10089492", title="Classifying a protein in the {CATH} database of domain structures", journal="Acta Crystallographica", volume="D54", pages="1155-1167", pdf="pdf/classifying.pdf" } @article{liu:finemapping, author="Liu, Z. and Song, D. and Kramer, A. and Martin, A.C.R. and Dandekar, T. and Schneider-Mergener, J. and Bautz, E.K.F. and Duebel, S.", year=1999, pmid="10398401", title="Fine mapping of the antigen-antibody interaction of {scFv215}, a recombinant antibody inhibiting {RNA} polymerase~{II} from {\emph{Drosophila melanogaster}}", journal="Journal of Molecular Recognition", volume="12", pages="103-111", pdf="pdf/liu.pdf" } @article{orengo:cath, author="Orengo, C.A. and Pearl, F.M. and Bray J.E. and Todd, A.E. and Martin, A.C.R. and Lo Conte, L. and Thornton, J.M.", year=1999, pmid="9847200", title="The {CATH} Database provides insights into protein structure/function relationships", journal="Nucleic Acids Research", volume="27", pages="275-279", pdf="pdf/cathnar.pdf" } @article{saldanha:backmutation, author="Saldanha, J.W. and Martin, A.C.R. and Leger, O.J.P.", year=1999, pmid="10593510", title="A single backmutation in the human {kIV} framework of a previously unsuccessfully humanized antibody restores the binding activity and increases the secretion in \emph{cos} cells", journal="Molecular Immunology", volume="36", pages="709-719", pdf="pdf/saldanha.pdf" } @article{pearl:cathassign, author="Pearl, F. and Todd, A.E. and Bray, J.E. and Martin, A.C.R. and Salamov, A.A. and Suwa, M. and Swindells, M.B. and Thornton, J.M. and Orengo, C.A.", year=2000, pmid="10816141", title="Using the {CATH} domain database to assign structures and functions to the genome sequences", journal="Biochem. Soc. Trans", volume="28", pages="269-275", pubpdf="http://www.biochemsoctrans.org/content/28/2/269.full-text.pdf", pdf="pdf/PearlUsingCath.pdf" } @article{martin:upsanddowns, author="Martin, A.C.R.", year=2000, pmid="11239082", title="Ups and Downs of Protein Topology; Rapid Comparison of Protein Structure", journal="Protein Engineering", volume="13", pages="829-837", pdf="pdf/upsdowns.pdf" } @article{martin:p53, author="Martin, A.C.R. and Facchiano, A.M. and Cuff, A.L. and Hernandez-Boussard, T. and Olivier, M. and Hainaut, P. and Thornton, J.M.", year=2002, pmid="11793474", title="Mutation Data and Structural Analysis of the p53 Tumour-Suppressor Protein", journal="Human Mutation", volume="19", pages="149-164", pdf="freepdf/p53_hummut.pdf" } @article{allcorn:sacs, author="Allcorn, L.C. and Martin, A.C.R.", year=2002, pmid="11836226", title="{SACS} - A Self-Maintaining Database of Antibody Crystal Structures", journal="Bioinformatics", volume="18", pages="175-181", pdf="pdf/sacs.pdf" } @article{kwok:g6pd, author="Kwok, C.H.Y. and Au, S.W.N. and Martin, A.C.R. and Lam, V.M.S.", year=2002, pmid="11857737", title="{G6PDdb}: An Integrated Database of Glucose-6-Phosphate Dehydrogenase ({G6PD}) Mutations", journal="Human Mutation", volume="19", pages="217-224", pdf="pdf/G6PD.pdf" } @article{collis:acs, author="Collis, A.V.J. and Brouwer, A.R. and Martin, A.C.R.", year=2003, pmid="12488099", title="Analysis of the Antigen Combining Site - Correlations Between Length and Sequence Composition of the Hypervariable Loops and the Nature of the Antigen", journal="J. Mol. Biol", volume="325", pages="337-354", pdf="pdf/collis.pdf" } @article{krauss:anticd22, author="Krauss, J. and Arndt, M.A.E. and Martin, A.C.R. and Liu, H. and Rybak, S.M.", year=2003, pmid="14600205", title="Specificity grafting of human antibody frameworks selected from a phage display library: generation of a highly stable humanized anti-{CD22} single chain {Fv} fragment", journal="Protein Engineering", volume="16", pages="753-759", pdf="pdf/krauss.pdf" } @article{harvey:flu, author="Harvey, R. and Zambon, M. and Martin, A.C.R. and Barclay, W.S.", year=2004, pmid="14671130", title="Restrictions to the adaptation of Influenza~{A} Virus {H5} haemagglutinin to the Human host", journal="Journal of Virology", volume="78", pages="502-507", pdf="pdf/harvey.pdf" } @article{martin:pdbsprotec, author="Martin, A.C.R.", year=2004, pmid="14764547", title="{PDBSprotEC}: A Web-accessible database linking {PDB} chains to {EC} numbers via {SwissProt}", journal="Bioinformatics", volume="20", pages="986-988", pubpdf="http://bioinformatics.oupjournals.org/cgi/content/abstract/bth048?ijkey=47kj35UBnMohU&keytype=ref", pdf="freepdf/pdbsprotec.pdf" } @article{cuff:voids, author="Cuff, A.L. and Martin, A.C.R.", year=2004, pmid="15561139", title="Analysis of Void Volumes in Proteins and Application to Stability of the p53 Tumour Suppressor Protein", journal="J. Mol. Biol", volume="344", pages="1199-1209", pdf="pdf/CuffMartinVoids.pdf" } @article{cavallo:mappingsnps, author="Cavallo, A. and Martin, A.C.R.", year=2005, pmid="15613399", title="Mapping {SNPs} to Protein Sequence and Structure Data", journal="Bioinformatics", volume="21", pages="1443-1450", subpdf="pdf/CavalloMartin.pdf", pubpdf="http://bioinformatics.oupjournals.org/cgi/content/abstract/bti220?ijkey=75YDqw49JgUOg&keytype=ref" } @article{martin:pdbsws, author="Martin, A.C.R.", year=2005, pmid="16188924", title="Mapping {PDB} chains to {UniProtKB} entries", journal="Bioinformatics", volume="21", pages="4297-4301", subpdf="freepdf/pdbsws.pdf", pdf="pdf/MartinMapping.pdf", pubpdf="https://academic.oup.com/bioinformatics/article/21/23/4297/194996" } @article{fooks:betasheets, author="Fooks, H.M. and Martin, A.C.R. and Woolfson, D.N. and Sessions, R.B. and Hutchinson, E.G.", year=2006, pmid="16337654", title="Amino acid pairing preferences in parallel beta-sheets in proteins", journal="J. Mol. Biol", volume="356", pages="32-44", pdf="pdf/fooks.pdf", web="/rubic/betapairprefs/" } @article{deevi:apat, author="Deevi, S.V.V. and Martin, A.C.R.", year=2006, pmid="16339285", title="An extensible automated protein annotation tool: standardizing input and output using validated {XML}", journal="Bioinformatics", volume="22", pages="291-296", pdf="pdf/apat-paper.pdf", pubpdf="https://doi.org/10.1093/bioinformatics/bti808", doi="10.1093/bioinformatics/bti808", web="/apat/" } @article{cuff:hbonds, author="Cuff, A.L. and Janes, R.W. and Martin, A.C.R.", year=2006, pmid="16601005", title="Analysing the Ability to Retain Sidechain Hydrogen-bonds in Mutant Proteins", journal="Bioinformatics", volume="22", pages="1464-1470", subpdf="/hbonds/paper.pdf", pdf="pdf/CuffHBonds.pdf", pubpdf="http://bioinformatics.oxfordjournals.org/cgi/reprint/btl120?ijkey=0B5PbmWKsNs3l7Q&keytype=ref", web="/hbonds/" } @article{merelli:agents, author="Merelli, E. and Armano, G. and Cannata, N. and Corradini, F. and d'Inverno, M. and Doms, A. and Lord, P. and Martin, A. and Milanesi, L. and Moeller, S. and Schroeder, M. and Luck, M.", year=2007, pmid="16772270", title="Agents in Bioinformatics, Computational and Systems Biology", journal="Briefings in Bioinformatics", volume="8", pages="45-59", pubpdf="http://bib.oxfordjournals.org/cgi/reprint/8/1/45?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=martin&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT", subpdf="freepdf/AgentBriefings.pdf", pdf="pdf/Agents_BIB.pdf" } @article{abhinandan:humanness, author="Abhinandan, K.R. and Martin, A.C.R.", year=2007, pmid="17442342", title="Analyzing the `degree of humanness' of antibody sequences", journal="J. Mol. Biol", volume="369", pages="852-862", doi="10.1016/j.jmb.2007.02.100", pdf="pdf/humanness.pdf", suppmat="freepdf/HumannessSupplementaryMaterial.pdf" } @article{churamani:adprobosylcyclase, author="Churamani, D. and Boulware, M.J. and Geach, T.J. and Martin, A.C.R. and Moy, G.W. and Su, Y.-H. and Vacquier, V.D. and Marchant, J.S. and Dale, L. and Patel, S.", year=2007, pmid="17726527", title="Molecular and Functional Characterization of a Novel Intracellular {ADP}-ribosyl cyclase", journal="PLoS ONE", volume="2(8)", pages="e797", doi="10.1371/journal.pone.0000797", pubpdf="17726527", subpdf="pdf/sandip1.pdf" } @article{abhinandan:abnum, author="Abhinandan, K.R. and Martin, A.C.R.", year=2008, pmid="18614234", title="Analysis and improvements to {Kabat} and structurally correct numbering of antibody variable domains", journal="Molecular Immunology", volume="45", pages="3832-3839", subpdf="freepdf/numbering.pdf", doi="10.1016/j.molimm.2008.05.022", pdf="pdf/numbering.pdf" } @article{mcmillan:fosta, author="McMillan, L.E.M. and Martin, A.C.R.", year=2008, pmid="18838004", title="Automatically extracting functionally equivalent proteins from {SwissProt}", journal="BMC Bioinformatics", volume="9", pages="418", pubpdf="http://www.biomedcentral.com/1471-2105/9/418", pdf="freepdf/fosta.pdf" } @article{churamani:adpribosylcyclase, author="Churamani, D. and Boulware, M. and Ramakrishnan, L. and Geach, T. and Martin, A.C.R. and Vacquier, V. and Marchant, J. and Dale, L. and Patel, S.", year=2008, pmid="18824228", title="Molecular characterisation of a novel cell surface {ADP}-ribosyl cyclase from the sea urchin", journal="Cellular Signalling", volume="20", pages="2347-2355", pdf="pdf/churamani.pdf" } @article{hurst:saapdb, author="Hurst, J.M. and McMillan, L.E.M. and Porter, C.T. and Allen, J. Fakorede, A. and Martin, A.C.R.", year=2009, pmid="19191322", title="The {SAAPdb} web resource: a large scale structural analysis of mutant proteins", journal="Human Mutation", volume="30", pages="616-624", subpdf="freepdf/SAAPdb.pdf", pdf="pdf/saapdb.pdf", suppmat="pdf/saapdb_sm001.pdf" } @article{izarzugaza:3dsim, author="Izarzugaza, J.M.G. and Baresic, A. and McMillan, L.E.M. and Yeats, C. and Clegg, A. and Orengo, C.A. and Martin, A.C.R. and Valencia, A.", year=2009, pmid="19758469", title="An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of {CATH} and {Gene3D}", journal="BMC Bioinformatics", volume="10 Suppl 8", pages="S5-S5", pdf="freepdf/izarzugaza2009.pdf", web="http://3dsim.bioinfo.cnio.es/" } @article{barasic:cpds, author="Baresic, A. and McMillan, L.E.M. and Rogers, H.H. and Hurst, J.M. and Martin, A.C.R.", year=2010, pmid="19900462", title="Compensated pathogenic deviations: analysis of structural effects", journal="Journal of Molecular Biology", volume="396", pages="19-30", doi="10.1016/j.jmb.2009.11.002", subpdf="freepdf/cpd_submit.pdf", pdf="pdf/cpd.pdf", suppmat="cpds/" } @article{thullier:macaque, author="Thullier, P. and Huish, O. and Pelat, T. and Martin, A.C.R.", year=2010, pmid="20043919", title="The humanness of macaque antibody sequences", journal="Journal of Molecular Biology", volume="396", pages="1439-1450", doi="10.1016/j.jmb.2009.12.041", subpdf="freepdf/macaque_submit.pdf", pdf="pdf/macaque.pdf" } @article{hirtreiter:spt45, author="Hirtreiter, A. and Damska, G.E. and Cheung, A. and Klose, D. and Grohmann, D. and Vojnic, E. and Martin, A.C.R. and Cramer, P. and Werner, F.", year=2010, pmid="20197319", title="{Spt4/5} Stimulates Transcription Elongation Through The {RNA} Polymerase Clamp Coiled Coil Motif", journal="Nucleic Acids Research", volume="38", pages="4040-4051", doi="10.1093/nar/gkq135", pdf="pdf/hirtreiter2010b.pdf" } @article{abhinandan:vhvlpacking, author="Abhinandan, K.R. and Martin, A.C.R.", year=2010, pmid="20591902", title="Analysis and Prediction of {VH/VL} Packing in Antibodies", journal="Protein Engineering Design and Selection", volume="23", pages="689-697", doi="10.1093/protein/gzq043", subpdf="freepdf/abhi_packing.pdf", pubpdf="http://peds.oxfordjournals.org/cgi/reprint/gzq043?ijkey=6zvl0Pm1bzSutNy&keytype=ref", pdf="pdf/abhi_packing.pdf" } @article{nan:factorh, author="Nan, R. and Farabella, I. and Schumacher, F.F. and Miller, A. and Gor, J. and Martin, A.C.R. and Jones, D.T. and Lengyel, I. and Perkins, S.J.", year=2011, pmid="21396937", title="Zinc binding to the Tyr402 and His402 allotypes of complement factor~{H}: possible implications for age-related macular degeneration", journal="J. Mol. Biol", volume="408", pages="714-735", subpdf="freepdf/HomoFH_Zn_v08.pdf", pdf="freepdf/nan_2011.pdf" } @article{izarzugaza:germlinedeviations, author="Izarzugaza, J.M.G. and Hopcroft, L.E.M. and Baresic, A. and Orengo, C.A. and Martin, A.C.R. and Valencia, A.", year=2011, pmid="21992016", title="Characterization of Pathogenic Germline Deviations in Human Protein Kinases", journal="BMC Bioinformatics", volume="12 Suppl.4", pages="S1", note="Special Issue - Proceedings of the European Conference on Computational Biology (ECCB) 2010 Workshop: Annotation, interpretation and management of mutation (AIMM-2010)", url="http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-645/", pubpdf="http://www.biomedcentral.com/1471-2105/12/S4/S1 [BMC]; http://ceur-ws.org/Vol-645/Paper3.pdf [AIMM-2010]", pdf="freepdf/izarzugaza_etal_2011.pdf", subpdf="freepdf/Izarzugaza-CharacterizingPathogenicGermlineDeviationsInHumanProteinKinases.pdf", suppmat="freepdf/izarzugaza_etal_2011_suppl.pdf" } @article{jayaram:germlinepairing, author="Jayaram, N. and Bhowmick, P. and Martin, A.C.R.", year=2012, pmid="22802295", title="Germline {VH/VL} Pairing in Antibodies", journal="Protein Engineering Design and Selection", volume="25", pages="523-530", doi="10.1093/protein/gzs043", subpdf="freepdf/chainpairing.pdf", pubpdf="http://peds.oxfordjournals.org/cgi/reprint/gzs043?ijkey=VadmYbFUBlVyI3z&keytype=ref", pdf="pdf/Jayaram_Bhowmick_Martin_2012_GermlineVhVlPairingInAntibodies_PEDS.pdf", suppmat="./chainpairing/" } @article{usifo:ldlr, author="Usifo, E. and Leigh, S.E.A. and Whittall, R.A. and Lench, N. and Taylor, A. and Yeats, C. and Orengo, C.A. and Martin, A.C.R. and Celli, J. and Humphries, S.E.", year=2012, pmid="22881376", title="Low Density Lipoprotein Receptor Gene Familial Hypercholesterolemia Variant Database: update and pathological assessment", journal="Annals of Human Genetics", volume="76", pages="387-401", doi="10.1111/j.1469-1809.2012.00724.x", pdf="pdf/UsifoLDLR.pdf" } @article{osborne:arsenite, author="Osborne, T. and Heath, M. and Martin, A.C.R. and Pankowski, J. and Hudson-Edwards, K. and Santini, J.", year=2013, pmid="23150098", title="Cold-adapted arsenite oxidase from a psychrotolerant {\emph{Polaromonas}} species", journal="Metallomics", volume="5", pages="318-324", doi="10.1039/c2mt20180a", pdf="pdf/osborne_heath_martin_pankowski_hudon-edwards_santini_2012_ColdAdaptedArseniteOxidaseFromAPsychrotolerantPolaromonasSpecies_Metallomics.pdf", } @article{alnumair:saappred, author="Al-Numair, N.S. and Martin, A.C.R.", year=2013, pmid="20591902", title="The {SAAP} pipeline and database: tools to analyze the impact and predict the pathogenicity of mutations", journal="BMC Genomics (ISMB 2012 SNP-SIG Special Issue)", volume="14(Suppl 3)", pages="S4", pubpdf="http://www.biomedcentral.com/1471-2164/14/S3/S4", pdf="freepdf/Alnumair_Martin_2013_SAAPPred_BMCGenomics.pdf" } @article{martin:jsav, author="Martin, A.C.R.", year=2014, pmid="25653836", title="Viewing multiple sequence alignments with the {J}avaScript Sequence Alignment Viewer ({JSAV})", journal="F1000Research", volume="3", pages="249", doi="10.12688/f1000research.5486.1", pubpdf="http://f1000research.com/articles/3-249/", pdf="freepdf/JSAV.pdf" } @article{martin:moonlightingabs, author="Martin, A.C.R.", year=2014, pmid="25399593", title="Structural Biology of Moonlighting - Lessons from Antibodies", journal="Biochem Soc Trans", volume="42", pages="1704-1708", subpdf="freepdf/Moonlighting_BiochemSocTrans_2014.pdf", pdf="pdf/MartinMoonlightingAbs2014.pdf", pubpdf="http://www.biochemsoctrans.org/bst/042/1704/0421704.pdf" } @article{henderson:moonlightingnewfactor, author="Henderson, B. and Martin, A.C.R.", year=2014, pmid="25399588", title="Protein Moonlighting: A New Factor in Biology and Medicine", journal="Biochem. Soc. Trans.", volume="42", pages="1671-1678", pdf="pdf/HendersonMartinMoonlighting2014.pdf", pubpdf="http://www.biochemsoctrans.org/bst/042/1671/0421671.pdf" } @article{porter:bioplib, author="Porter, C.T. and Martin, A.C.R.", year=2015, pmid="26323716", title="{BiopLib} and {BiopTools} - a {C} programming library and toolset for manipulating protein structure (Application Note)", journal="Bioinformatics", volume="31", pages="4017-4019", subpdf="freepdf/bioplib.pdf", pdf="freepdf/Porter_Martin_2015_BioplibAndBioptoolsACProgrammingLibraryAndToolsetForManipulatingProteinStructure_Bioinformatics.pdf", pubpdf="http://bioinformatics.oxfordjournals.org/content/31/24/4017.full.pdf+html" } @article{martin:specieserrors, author="Martin, A.C.R. and Rees, A.R.", year=2016, pmid="27274090", title="Extracting human antibody sequences from public databases for antibody humanization: high frequency of species assignment errors", journal="Protein Engineering Design and Selection", volume="29", pages="403-408", subpdf="freepdf/AntibodyAnnotation2016_AsAccepted.pdf", pdf="pdf/AntibodyAnnotation2016.pdf", pubpdf="http://peds.oxfordjournals.org/content/early/2016/06/03/protein.gzw018.full.pdf+html", suppmat="AntibodyAnnotation/" } @article{alnumair:myh7, author="Al-Numair, N.S. and Lopes, L. and Syrris, P. and Monserrat, L. and Elliott, P. and Martin, A.C.R.", year=2016, pmid="27318203", title="The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain ({Myosin-7}) missense variants", journal="Bioinformatics", volume="32", pages="2947-2955", doi="10.1093/bioinformatics/btw362", pdf="pdf/MYH7.pdf", subpdf="freepdf/myh7_030516.pdf", suppmat="freepdf/MYH7/" } @article{jayaram:tfbs, author="Jayaram, N. and Usvyat, D. and Martin, A.C.R.", year=2016, pmid="27806697", title="Evaluating tools for transcription factor binding site prediction", journal="BMC Bioinformatics", doi="10.1186/s12859-016-1298-9", subpdf="freepdf/tfbs.pdf", pubpdf="http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1298-9", suppmat="tfbs/" } @article{swindells:abysis, author="Swindells, M.B. and Porter, C.T. and Couch, M. and Hurst, J. and Abhinandan, K.R. and Nielsen, J.H. and Macindoe, G. and Hetherington, J. and Martin, A.C.R.", year=2017, pmid="27561707", title="{abYsis}: Integrated Antibody Sequence and Structure - Management, Analysis and Prediction", journal="Journal of Molecular Biology", volume="429", pages="356-364", subpdf="freepdf/abysis.pdf", pdf="pdf/abysis.pdf" } @article{northey:intpred, author="Northey, T. and Baresic, A. and Martin, A.C.R.", year=2017, pmid="28968673", title="{IntPred}: a structure-based predictor of protein-protein interaction sites", journal="Bioinformatics", volume=34, pages="223--229", doi="10.1093/bioinformatics/btx585", subpdf="freepdf/intpred.pdf", pubpdf="https://academic.oup.com/bioinformatics/article-pdf/34/2/223/23154608/btx585.pdf", suppmat="intpred/" } @article{ferdous:abdb, author="Ferdous, S. and Martin, A.C.R.", year="2018", volume="2018", pages="bay040", title="{AbDb}: Antibody structure database - A database of {PDB} derived antibody structures", journal="Database", subpdf="freepdf/AbDb_AsSubmitted.pdf", doi="10.1093/database/bay040", pubpdf="https://academic.oup.com/database/article-pdf/doi/10.1093/database/bay040/24755385/bay040.pdf?guestAccessKey=0f5e6e34-0824-406d-9f56-f2e6b743bf5b", pdf="pdf/Ferdous_Martin_2018_AbDb.pdf" } @article{cheetham:molmodacs, author="Cheetham, J.C. and Roberts, S. and Martin, A.C.R. and Rees, A.R.", type="meeting abstract", year=1987, title="Molecular Modelling of Antibody Combining Sites", journal="Protein Engineering", volume="1", pages="232-233", pdf="pdf/Cheetham_Roberts_Martin_Rees_1987_MolecularModellingOfAntibodyCombiningSites_ProteinEngineering87Proceedings.pdf" } @misc{rees:3dpredacs, type="meeting abstract", author="Rees, A.R. and Martin, A.C.R. and Cheetham, J.C. and Webster, D.", year=1989, title="Prediction of three-dimensional structure of antibody combining sites.", journal="Proceedings of the Sixth European Seminar and Exhibition on Computer-Aided Molecular Design 5th-6th October, 1989, (IBC Press)", pdf="pdf/six_euro.pdf" } @incollection{rees:combsitemolmod, author="Rees, A.R. and Martin, A.C.R. and Roberts, S. and Cheetham, J.C.", year=1989, title="Combining sites and epitopes defined by molecular modelling, protein engineering and {NMR}", booktitle="Proceedings of the {UCLA} Symposia on Molecular and Cellular Biology: Protein and Pharmaceutical Engineering", bookurl="https://books.google.co.uk/books/about/Protein_and_pharmaceutical_engineering.html?id=vkpLAQAAIAAJ&redir_esc=y", pages="35-54", editor="Craik, C. and Fletterick, R. and Matthews, C.R. and Wells, J.", publisher="Liss", address="New York", note="ISBN: 047156771X, 9780471567714" } @article{rees:acspreddes, type="meeting abstract", author="Rees, A.R. and Martin, A.C.R. and Webster, D.M. and Cheetham, J.C. and and Roberts, S.", year=1990, title="Antibody Combining Sites: Prediction and Design", journal="Biophysical J", volume="57", pages="A384", note="(Thirty-Fourth Annual Meeting of the Biophysical Society, February 18-22, 1990 Baltimore Convention Center Baltimore, Maryland)", pdf="freepdf/biochemj1990.pdf" } @article{gregory:acspreddes, type="review", author="Gregory, D.St.J. and Staunton, D. and Martin, A.C.R. and Cheetham, J.C. and Pedersen, J.T. and Rees, A.R.", year=1990, pmid="2099739", title="Antibody combining sites - Prediction and design", journal="Biochemical Society Symposium", volume="57", pages="147-155" } @article{martin:molmodacs, author="Martin, A.C.R. and Cheetham, J.C. and Rees, A.R.", year=1991, pmid="1762554", title="Molecular modelling of antibody combining sites", journal="Methods in Enzymology", volume="203", pages="121-153", pdf="pdf/methenz.pdf" } @article{martin:approachpers, type="review", author="Martin, A.C.R.", year=1994, pmid="7841988", title="Modelling antibodies: Approach and perspective", journal="Lupus", volume="3", pages="365-366", pdf="pdf/approach_perspec.pdf" } @article{kalsi:sfantidna, type="review", author="Kalsi, J.K. and Martin, A.C.R. and Isenberg, D.A.", year=1995, pmid="8528217", title="Structure-function relation of anti-{DNA} antibodies", journal="Lupus", volume="4", pages="245-248", pdf="pdf/strucfunc.pdf" } @article{martin:abmodabs, type="meeting abstract", author="Martin, A.C.R. and MacCallum, R.M. and Thornton, J.M.", year=1995, title="Analysis and modelling of antibodies", journal="Immunology", volume="86 Suppl 1", pages="95" } @incollection{jones:protdomfoldfunc, author="Jones, S. and Martin, A.C.R. and Karmirantzou, M. and Laskowski, R.A. and Orengo, C. and Thornton, J.M.", year=1997, title="Protein Domains, Folds and Functions", booktitle="Transactions of the American Crystallography Association", bookurl="http://www.amercrystalassn.org/content/pages/main-transactions", volume="32, `Structural Informatics'", editor="Gilliland, G. and Berman, H.", publisher="American Crystollographic Association" } @article{ravirajan:correctdnabind, type="correction", author="Ravirajan, C.T. and Rahman, M.A. and Papadaki, L. and Griffiths, M.H. and Kalsi, J. and Martin, A.C.R. and Ehrenstein, M.R. and Latchman, D.S. and Isenberg, D.A.", year=1999, title="Correction: Genetic, structural and functional properties of an {IgG} {DNA}-binding monoclonal antibody from a lupus patient with nephritis ({E}uropean {J}ournal of {I}mmunology 28(1998)339-350)", journal="European Journal of Immunology", volume="29", pages="3052" } @article{martin:bookrevsimnulation, type="book review", author="Martin, A.C.R.", year=2000, title="A practical introduction to the simulation of molecular systems", journal="Computers and Chemistry", volume="24", pages="239-240", pdf="pdf/simulation.pdf" } @article{martin:genedata, type="correspondence", author="Martin, A.C.R.", year=2000, title="Model already exists for fair use of gene data", journal="Nature", volume="406", pages="933", pdf="pdf/model_exists_nature.pdf" } @article{martin:bookrevmodelling, type="book review", author="Martin, A.C.R.", year=2001, title="Modelling Molecular Structures", journal="Computers and Chemistry", volume="25", pages="309-310", pdf="pdf/modmolstruc.pdf" } @article{martin:integrate, type="meeting report", author="Martin, A.C.R.", year=2001, title="Can we integrate bioinformatics data on the internet?", journal="Trends in Biotechnology", volume="19", pages="327-328", pdf="pdf/TIBTECH0901.pdf" } @article{corne:aibioinf, type="editorial", author="Corne, D.W. and Martin, A.C.R.", year=2001, title="Aritificial Intelligence in Bioinformatics", journal="Computers and Chemistry", volume="26", pages="1-3", note="Special issue edited by Martin and Corne", pdf="pdf/AISB_editorial.pdf" } @article{barasic:cpdrev, type="review", author="Baresic, A. and Martin, A.C.R.", year=2011, title="Compensated Pathogenic Mutations", journal="Biomolecular Concepts", volume="2", pages="281-292", doi="10.1515/BMC.2011.025", pubpdf="http://www.reference-global.com/doi/abs/10.1515/BMC.2011.025", pdf="pdf/CPDReview.pdf", subpdf="freepdf/CPDReview_small.pdf", pmid="25962036" } @article{henderson:virulence, type="review", author="Henderson, B. and Martin, A.C.R.", year=2011, pmid="21646455", title="Bacterial Virulence in the Moonlight: Multitasking Bacterial Moonlighting Proteins are Virulence Determinants in Infectious Disease", journal="Infection and Immunity", volume="79", pages="3476-91", doi="10.1128/IAI.00179-11", subpdf="freepdf/ProteinMoonlightingBacterialVirulence.pdf", pdf="pdf/HendersonMartin_2011_Moonlighting_IAI.pdf" } @article{henderson:bacterialmoonlighting, type="review", author="Henderson, B. and Martin, A.C.R.", year=2013, pmid="22143554", title="Bacterial Moonlighting Proteins and Bacterial Virulence", journal="Current Topics in Microbiology and Immunology", volume="358", pages="155-213", subpdf="freepdf/MoonlightingBacterialVirulenceSubmitted.pdf", doi="10.1007/82_2011_188" } @article{leigh:pcsk9update, author="Leigh, S.E.A. and Lee, Y.P. and Whittall, R.A. and Dawson, N. and Das, S. and Martin, A.C.R. and Orengo, C.A. and Humphries, S.E.", year=2014, url="http://www.atherosclerosis-journal.com/article/S0021-9150(14)00498-5/fulltext", title="Update and analysis of the {UCL} Pro-protein convertase subtilisin/kexin Type9 gene ({PCSK9}) variant database", journal="Atherosclerosis", volume="235", pages="E98", pdf="pdf/pcsk9_2014.pdf" } @article{ferdous:bceposter2, type="poster", author="Ferdous, S. and Martin, A.C.R.", year=2016, title="Exploration of conformational {B}-cell epitopes: components to peptide-based vaccines ({ECCB})", journal="F1000Research", volume="5", pages="2142", subpdf="freepdf/ECCB2016_f1000research-134786.pdf", doi="10.7490/f1000research.1112977.1" } @article{ferdous:bceposter1, type="poster", author="Ferdous, S. and Martin, A.C.R.", year=2015, title="Characterization and structural analysis of {B}-cell epitopes for vaccine and therapeutic antibody design ({ISMB})", journal="F1000Research", volume="4", pages="523", subpdf="freepdf/ISMB2015_f1000research-99927.pdf", doi="10.7490/f1000research.1110268.1" } @misc{martin:annaobituary, type="obituary", author="Martin, A.C.R.", year=2017, url="http://www.antibodysociety.org/anna-tramontano-memorium/", title="{A}nna {T}ramontano - In memorium", note="Obituary for the Antibody Society" } @misc{martin:cyrusobituary, type="obituary", author="Martin, A.C.R.", year=2019, url="https://www.antibodysociety.org/cyrus-chothia-in-memoriam/", title="{C}yrus {C}hothia - In memorium", note="Obituary for the Antibody Society" } @misc{martin:f1000krawczyk, type="F1000 recommendation", author="Martin, A.C.R.", year=2017, url="https://f1000.com/prime/contributor/evaluate/article/727250933", title="Recommendation: {I}mproving {B}-cell epitope prediction and its application to global antibody-antigen docking ({Krawczyk K, Liu X, Baker T, Shi J, Deane C.M.})", pdf="f1000/F1000_Krawczyk_2017.pdf" } @misc{martin:f1000weitznew, type="F1000 recommendation", author="Martin, A.C.R.", year=2017, url="https://f1000.com/prime/contributor/evaluate/article/727009604", title="Recommendation: {A}ccurate Structure Prediction of {CDR H3} Loops Enabled by a Novel Structure-Based {C}-Terminal Constraint ({Weitzner B.D., Gray J.J.})", pdf="f1000/F1000Weitzner_Gray_2017.pdf" } @misc{martin:f1000parren, type="F1000 recommendation", author="Martin, A.C.R.", year=2018, url="https://f1000.com/prime/727722934", title="Recommendation: {C}hanges to the {I}nternational {N}onproprietary {N}ames for antibody therapeutics 2017 and beyond: of mice, men and more ({Parren, P.W.H.I, Carter, P.J. and Pluckthun, A.})", pdf="f1000/F1000Parren_Carter_Plukthun_2018.pdf" } @misc{martin:f1000regep, type="F1000 recommendation", author="Martin, A.C.R.", year=2018, url="https://f1000.com/prime/727449083", title="Recommendataion: {T}he {H3} loop of antibodies shows unique structural characteristics", pdf="f1000/F1000Regep_Georges_Shi_Popovic_Deane_2017.pdf" } @incollection{martin:abanalysis, type="chapter", author="Martin, A.C.R.", year=2001, title="Protein Sequence and Structure Analysis of Antibody Variable Domains", bookurl="http://www.springeronline.com/sgw/cda/frontpage/0,10735,5-10030-22-1991398-0,00.html", booktitle="Antibody Engineering Lab Manual", editor="Duebel, S. and Kontermann, R.", publisher="Springer-Verlag", address="Heidelberg" } @incollection{martin:compmod, type="chapter", author="Martin, A.C.R.", year=2002, title="Comparative Modelling", bookurl="http://www.amazon.co.uk/exec/obidos/ASIN/1859960545/", booktitle="Bioinformatics", editor="Orengo, C.A. and Jones, D.T. and Thornton, J.M.", publisher="Bios Scientific Publishers", address="Oxford", note="ISBN: 1859960545" } @incollection{martin:internettech, type="chapter", author="Martin, A.C.R.", year=2002, title="Internet Technologies for Bioinformatics", bookurl="http://www.amazon.co.uk/exec/obidos/ASIN/1859960545/", booktitle="Bioinformatics", editor="Orengo, C.A. and Jones, D.T. and Thornton, J.M.", publisher="Bios Scientific Publishers", address="Oxford", note="ISBN: 1859960545" } @incollection{martin:abengtoos, type="chapter", author="Martin, A.C.R. and Allen, J.", year=2007, title="Bioinformatics tools for antibody engineering", bookurl="http://www.wiley-vch.de/publish/en/books/bySubjectLS00/ISBN3-527-31453-9/", booktitle="Handbook of Therapeutic Antibodies Vol 1, {T}echnologies", editor="Duebel, S.", publisher="Wiley-VCH", address="Weinheim", note="ISBN-10: 3-527-31453-9", subpdf="pdf/MartinAllen.pdf" } @incollection{martin:abanalysistools, type="chapter", author="Martin, A.C.R.", year=2010, title="Protein Sequence and Structure Analysis of Antibody Variable Domains", bookurl="http://www.springer.com/new+%26+forthcoming+titles+%28default%29/book/978-3-642-01146-7", booktitle="Antibody Engineering Lab Manual Volume 2 (2nd Edition)", editor="Duebel, S. and Kontermann, R.", publisher="Springer-Verlag", address="Heidelberg", note="ISBN-10: 3642011462, ISBN-13: 978-3642011467", subpdf="freepdf/AntibodyEngineeringChapterEdition2.pdf" } @incollection{martin:snpimpact, type="chapter", author="Martin, A.C.R. and Baresic, A.", year=2013, title="Structural Impact of {SNPs}", bookurl="http://www.springer.com/gb/book/9783642167119", booktitle="Encyclopedia of Biophysics", editor="Roberts, G.K.", note="ISBN 978-3-642-16711-9.", subpdf="pdf/StructuralEffectsOfSNPsV1.pdf", publisher="Springer-Verlag", address="Berlin Heidelberg" } @incollection{martin:abengtools2, type="chapter", author="Martin, A.C.R. and Allen, J.", year=2014, title="Bioinformatics tools for antibody engineering", booktitle="Handbook of Therapeutic Antibodies Vol 1, {T}echnologies (2nd Edition)", bookurl="https://www.wiley.com/en-gb/Handbook+of+Therapeutic+Antibodies,+2nd+Edition-p-9783527329373", editor="Duebel, S. and Reichert, J.", publisher="Wiley-Blackwell", address="Weinheim", note="ISBN-10: 3527329374, ISBN-13: 978-3527329373", subpdf="pdf/MartinAllen2.pdf" } @incollection{martin:introprot, type="chapter", author="Martin, A.C.R.", year=2017, title="An introduction to the protein molecule", booktitle="Protein Moonlighting in Biology and Medicine, the Biological and Biomedical Consequences of Protein Moonlighting", editor="Henderson, B. and Fares, M.A. and Martin, A.C.R.", publisher="Wiley-Blackwell", address="Hoboken, New Jersey", note="Chapter 1. ISBN-10: 1118952081; ISBN-13: 978-1118952085", subpdf="pdf/MoonlightingBook_Chapter1_TheProteinMolecule.pdf" } @incollection{martin:structmoonlighting, type="chapter", author="Martin, A.C.R.", year=2017, title="The structural basis of protein moonlighting", booktitle="Protein Moonlighting in Biology and Medicine, the Biological and Biomedical Consequences of Protein Moonlighting", editor="Henderson, B. and Fares, M.A. and Martin, A.C.R.", publisher="Wiley-Blackwell", address="Hoboken, New Jersey", note="Chapter 4. ISBN-10: 1118952081; ISBN-13: 978-1118952085", subpdf="pdf/MoonlightingBook_Chapter4_StructuralBasisOfMoonlighting.pdf" } @misc{rybak:humpatent, type="patent", author="Rybak, S. and Krauss, J. and Arndt, M. and Martin, A.C.R.", year=2003, url="http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=7456260.PN.&OS=PN/7456260&RS=PN/7456260", title="Specificity grafting of a murine antibody onto a human framework", note="US Patent 7,456,260. Issued 25 Nov 2008. (Priority date 17 June 2002)", pct="PCT/US03/1933 WO03105782", pcturl="http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO03105782&F=0", } @misc{rybak:humpatenteu, type="patent", author="Rybak, S. and Krauss, J. and Arndt, M. and Martin, A.C.R.", year=2003, url="https://europepmc.org/article/pat/ep1551453", title="Specificity grafting of a murine antibody onto a human framework", note="EU Patent EP1551453 equivalent of US7,456,260", pcturl="https://worldwide.espacenet.com/publicationDetails/biblio?FT=D&date=20050713&DB=&locale=en_EP&CC=EP&NR=1551453A2&KC=A2&ND=1" } @misc{martin:xmaspatent, type="patent", author="Martin, A.C.R.", year=2000, url="http://v3.espacenet.com/textdoc?DB=EPODOC&IDX=WO0169413&F=0", title="Process for storing data", pct="PCT/GB01/01123; WO2001/069413; WO0169413", pcturl="http://l2.espacenet.com/espacenet/bnsviewer?CY=gb&LG=en&DB=EPD&PN=WO0169413&ID=WO+++0169413A2+I+", note="US Patent US2004030502 application priority date 14 March 2000" } @incollection{martin:snpimpact2, type="chapter", author="Martin, A.C.R. and Baresic, A. and Al-Numair, N.", title="Structural Impact of Single Nucleotide Variations ({SNVs})", year="2018", bookurl="http://www.springer.com/gb/book/9783642167119", booktitle="Encyclopedia of Biophysics", edition="2nd", editor="Roberts, G.K. and Watts, A.", note="ISBN 978-3-642-16711-9", subpdf="pdf/StructuralEffectsOfSNPsV2.pdf", pdf="pdf/Martin2018EffectsOfSNVs.pdf", publisher="Springer-Verlag", address="Berlin Heidelberg", doi="10.1007/978-3-642-35943-9_430-1" } @article{arndt:humanizeddiabody, author="Arndt, Michaela and Vu, Bang K. and Martin, Andrew C.R. and Liu, Huaitian and Newton, Dianne L. and Seeber, Siegfried and Rybak, Susanna M. and Krauss, Jurgen", type="meeting abstract", year=2006, title="A Humanized Diabody-Ribonuclease Fusion Protein Mediates Potent and Selective Killing of {CD22}-Positive Tumor Cells", journal="Journal of Immunotherapy", volume=29, pages="671", doi="10.1097/01.cji.0000211343.73588.59", pubpdf="https://journals.lww.com/immunotherapy-journal/Citation/2006/11000/A_Humanized_Diabody_Ribonuclease_Fusion_Protein.147.aspx", pdf="pdf/arndt2006.pdf" } @article{ireland:zincbind, author = "Ireland, S.M. and Martin, A.C.R.", year = "2019", title = "{ZincBind} --- The Database of Zinc Binding Sites", journal = "Database", doi="10.1093/database/baz006", pubpdf="https://academic.oup.com/database/article/doi/10.1093/database/baz006/5304468?guestAccessKey=1ba32d17-6f64-4079-a17e-779215d7aa04", pdf="freepdf/Ireland_Martin_2019_ZincBind.pdf", subpdf="freepdf/ZincBind.pdf", web="http://zincbind.bioinf.org.uk/" } @article{ferdous:epitopeanalysis, author = "Ferdous, S. and Kelm, S. and Baker, T.S. and Shi, J. and Martin, A.C.R.", year = "2019", volume = 114, pages = "643--650", title = "B-cell Epitopes: {D}iscontinuity and Conformational Analysis", journal = "Molecular Immunology", subpdf="freepdf/EpitopeAnalysis.pdf", suppmat="freepdf/EpitopeAnalysis_SuppMat.pdf", doi="10.1016/j.molimm.2019.09.014" } @article{ireland:atomium, author = "Ireland, S.M. and Martin, A.C.R.", year = "2020", volume = 36, pages = "2750--2754", title = "{atomium} --- A {P}ython Structure Parser", journal = "Bioinformatics", subpdf="freepdf/atomium_submitted.pdf", suppmat="freepdf/atomium_supplementary.pdf", pubpdf="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa072/5733721?guestAccessKey=80afcf84-8912-4127-83ff-dc42417bbfcb", doi="10.1093/bioinformatics/btaa072" } @article{ireland:zincbindpredict, author = "Ireland, S.M. and Martin, A.C.R.", year = "2021", volume=26, pages=966, title = "{ZincBindPredict} --- Prediction of Zinc Binding Sites in Proteins", journal = "Molecules", pubpdf="https://www.mdpi.com/1420-3049/26/4/966/", pdf="freepdf/ZincBindPredict.pdf", suppmat="freepdf/ZincBindPredict_supplementary.zip", web="http://zincbind.bioinf.org.uk/predict/", doi="10.3390/molecules26040966" } @article{martin:ucb, author="Martin, Andrew and Tyson, Kerry and Page, Matt and Fossati, Gianluca and Snowden, James and Abhinandan, Raghavan and Lawson, Alastair and Nesbitt, Andrew and Popplewell, Andrew", type="meeting abstract", year=2007, title="Comparison of Naturally Occurring Human Immunoglobulin Sequences with the Anti-TNF Agents Certolizumab Pegol, Adalimumab, and Infliximab", journal="Clinical Immunology", volume="123 Supp-S", Xpages="S170-S171", doi="10.1016/j.clim.2007.03.127", pdf="freepdf/MartinUCB2007.pdf" } @article{armano:aamas05, type="editorial", author="Armano, G. and Denzinger, J. and Martin, A. and Merelli, E. and Miles, S. and Tianfield, H. and Unland, R.", year=2005, title="First International Workshop on Multi-Agent Systems for Medicine, Computational Biology, and Bioinformatics", journal="Proceedings of the Fourth International Joint Conference on Autonomous Agents and Multi-agent Systems (AAMAS '05)", volume="2005", pages="preface", note="Workshop co-organizer", pubpdf="https://www.researchgate.net/publication/242386082_AAMAS_Workshop_on_Multi-Agent_Systems_for_Medicine_Computational_Biology_and_Bioinformatics_Preface", pdf="pdf/AAMAS_Workshop_on_Multi-Agent_Systems_for_Medicine.pdf" } @article{ireland:graphql, author = "Ireland, S.M. and Martin, A.C.R.", year = "2021", pages="vbab023", title = "{GraphQL} for the Delivery of Bioinformatics Web {APIs} and Application to {ZincBind}", journal = "Bioinformatics Advances", web="http://zincbind.bioinf.org.uk/", subpdf="freepdf/GraphQL_Proof.pdf", pdf="pdf/GraphQL.pdf", pubpdf="https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbab023/6377801", doi="10.1093/bioadv/vbab023" } @article{khetan:biopharminf, type="review", author = "Khetan, R. and Curtis, R. and Deane, C.M. and Hadsund, J.T. and Kar, U. and Krawczyk, K. and Kuroda, D. and Robinson, S.A. and Sormanni, P. and Tsumoto, K. and Warwicker, J. and Martin, A.C.R.", year = "2022", volume = "14", pages = "e2020082", title = "Current advances in Biopharmaceutical Informatics: Guidelines, impact and challenges in Computational Developability Assessment of antibody therapeutics", pdf="freepdf/KMAB-2021-0158R1_Khetan_FINAL.pdf", journal = "mAbs", pubpdf="https://www.tandfonline.com/doi/pdf/10.1080/19420862.2021.2020082", doi="10.1080/19420862.2021.2020082" } @article{koch:abnames, author = "Guimaraes Koch, S.S. and Thorpe, R. and Kawasaki, N. and Lefranc, M.-P. and Malan, S. and Martin, A.C.R. and Mignot, G. and Pluckthun, A. and Rizzi, M. and Shubat, S. and Weisser, K. and Balocco, R.", year = "2022", volume = "14", pages = "e2075078", title = "{I}nternational {N}onproprietary {N}ames ({INN}) for monoclonal antibodies: an evolving nomenclature system", subpdf="freepdf/Koch_mabnames_preprint.pdf", pdf="freepdf/Koch_mabnames.pdf", journal = "mAbs", doi="10.1080/19420862.2022.2075078" } @article{sweet-jones:abml, author = "Sweet-Jones, J. and Ahmad, M. and Martin, A.C.R.", year = "2022", title = "Antibody Markup Language ({AbML}) --- A Notation Language for Antibody-Based Drug Formats and Software for Creating and Rendering {AbML} ({abYdraw})", subpdf="freepdf/AbML_MAbs_Suppl.pdf", journal = "mAbs", volume = 14, pages = "e2101183", doi="10.1080/19420862.2022.2101183" } @article{boron:vhvl, author = "Boron, V.A. and Martin, A.C.R.", year = "2023", volume = "36", pages = "1--8", title = "{abYpap:} Improvements to the Prediction of Antibody {VH/VL} Packing Using Gradient Boosted Regression", subpdf = "freepdf/abypap.pdf", journal = "Protein Engineering Design and Selection", url = "https://academic.oup.com/peds/article/doi/10.1093/protein/gzad021/7453448", doi = "10.1093/protein/gzad021" } @article{lin:varipred, author = "Lin, W. and Wells, J. and Wang, Z. and Orengo, C. and Martin, A.C.R.", year = "2023", title = "{VariPred}: Enhancing Pathogenicity Prediction of Missense Variants Using Protein Language Models", subpdf = "freepdf/VariPred_AsSubmitted.pdf", journal = "Briefings in Bioinformatics", url = "https://www.biorxiv.org/content/10.1101/2023.03.16.532942v2.full.pdf", doi = "10.1101/2023.03.16.532942" } @article{liu:cdrflex, author = "Liu, C. and Denzler, L.M.A. and Hood, O.E.C. and Martin, A.C.R.", title = "Do antibody {CDR} loops change conformation upon binding?", year = "2024", volume = 16, issue = 1, pages = "2322533", subpdf = "freepdf/Liu_etal_DoCDRSChangeConformationOnBinding_AsAccepted.pdf", pdf = "freepdf/Liu_etal_DoCDRSChangeConformationOnBinding.pdf", journal = "mAbs", url = "https://www.tandfonline.com/doi/full/10.1080/19420862.2024.2322533", doi = "10.1080/19420862.2024.2322533" }