[Invited Lecture] Protein Folds and Functions. - Janet M. Thornton; Andrew C. R. Martin; Christine A. Orengo; Duncan Milburn; Roman A. Laskowski (German Conference on Bioinformatics, 1998)

Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania. - Fabio Zuccotto; Andrew C. R. Martin; Roman A. Laskowski; Janet M. Thornton; Ian H. Gilbert (J. Comput. Aided Mol. Des., 1998)

A Practical Introduction to the Simulation of Molecular Systems, Martin J. Field, Cambridge University Press, 1999; ISBN 0-521-58129-X. 325pp.. - Andrew C. R. Martin (Comput. Chem., 2000)

Modelling Molecular Structures, 2nd Ed, by Alan Hinchliffe, Wiley, 2000, ISBN 0-471-48993-X. - Andrew C. R. Martin (Comput. Chem., 2001)

SACS-Self-maintaining database of antibody crystal structure information. - Lee C. Allcorn; Andrew C. R. Martin (Bioinform., 2002)

Artificial Intelligence in Bioinformatics. - David Corne; Andrew C. R. Martin (Comput. Chem., 2002)

PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt. - Andrew C. R. Martin (Bioinform., 2004)

Mapping SNPs to protein sequence and structure data. - Antonio Cavallo; Andrew C. R. Martin (Bioinform., 2005)

Mapping PDB chains to UniProtKB entries. - Andrew C. R. Martin (Bioinform., 2005)

Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins. - Alison L. Cuff; Robert W. Janes; Andrew C. R. Martin (Bioinform., 2006)

An extensible automated protein annotation tool: standardizing input and output using validated XML. - S. Vishnu V. Deevi; Andrew C. R. Martin (Bioinform., 2006)

Agents in bioinformatics, computational and systems biology. - Emanuela Merelli; Giuliano Armano; Nicola Cannata; Flavio Corradini; Mark d'Inverno; Andreas Doms; Phillip W. Lord; Andrew C. R. Martin; Luciano Milanesi; Steffen Möller; Michael Schroeder 001; Michael Luck (Briefings Bioinform., 2007)

Automatically extracting functionally equivalent proteins from SwissProt. - Lisa E. M. McMillan; Andrew C. R. Martin (BMC Bioinform., 2008)

An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. - José M. G. Izarzugaza; Anja Baresic; Lisa E. M. McMillan; Corin Yeats; Andrew B. Clegg; Christine A. Orengo; Andrew C. R. Martin; Alfonso Valencia (BMC Bioinform., 2009)

Characterization of pathogenic germline mutations in human Protein Kinases. - José M. G. Izarzugaza; Lisa E. M. Hopcroft; Anja Baresic; Christine A. Orengo; Andrew C. R. Martin; Alfonso Valencia (BMC Bioinform., 2011)

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV). - Andrew C. R. Martin (F1000Research, 2014)

BiopLib and BiopTools - a C programming library and toolset for manipulating protein structure. - Craig T. Porter; Andrew C. R. Martin (Bioinform., 2015)

The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants. - Nouf S. Al-Numair; Luis Lopes 004; Petros Syrris; Lorenzo Monserrat; Perry Elliott; Andrew C. R. Martin (Bioinform., 2016)

Evaluating tools for transcription factor binding site prediction. - Narayan Jayaram; Daniel Usvyat; Andrew C. R. Martin (BMC Bioinform., 2016)

AbDb: antibody structure database - a database of PDB-derived antibody structures. - Saba Ferdous; Andrew C. R. Martin (Database J. Biol. Databases Curation, 2018)

IntPred: a structure-based predictor of protein-protein interaction sites. - Thomas C. Northey; Anja Baresic; Andrew C. R. Martin (Bioinform., 2018)

ZincBind - the database of zinc binding sites. - Sam M. Ireland; Andrew C. R. Martin (Database J. Biol. Databases Curation, 2019)

atomium - a Python structure parser. - Sam M. Ireland; Andrew C. R. Martin (Bioinform., 2020)

AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction. - Chunan Liu; Lilian Denzler; Yihong Chen; Andrew C. R. Martin; Brooks Paige (NeurIPS, 2024)

AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking. - Chunan Liu; Aurélien Pélissier; Yanjun Shao; Lilian Denzler; Andrew C. R. Martin; Brooks Paige; Mariia Rodriguez Martinez (CoRR, 2025)