MACiE: a database of enzyme reaction mechanisms. - Gemma L. Holliday; Gail J. Bartlett; Daniel E. Almonacid; Noel M. O'Boyle; Peter Murray-Rust; Janet M. Thornton; John B. O. Mitchell (Bioinform., 2005)

PYCHEM: a multivariate analysis package for python. - Roger M. Jarvis; David Broadhurst; Helen E. Johnson; Noel M. O'Boyle; Royston Goodacre (Bioinform., 2006)

Userscripts for the Life Sciences. - Egon L. Willighagen; Noel M. O'Boyle; Harini Gopalakrishnan; Dazhi Jiao; Rajarshi Guha; Christoph Steinbeck; David J. Wild 001 (BMC Bioinform., 2007)

Random Forest Models To Predict Aqueous Solubility. - David S. Palmer; Noel M. O'Boyle; Robert C. Glen; John B. O. Mitchell (J. Chem. Inf. Model., 2007)

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. - Gemma L. Holliday; Daniel E. Almonacid; Gail J. Bartlett; Noel M. O'Boyle; James W. Torrance; Peter Murray-Rust; John B. O. Mitchell; Janet M. Thornton (Nucleic Acids Res., 2007)

cclib: A library for package-independent computational chemistry algorithms. - Noel M. O'Boyle; Adam L. Tenderholt; Karol M. Langner (J. Comput. Chem., 2008)

Book Review of Gnuplot in Action. - Noel M. O'Boyle (J. Chem. Inf. Model., 2008)

Using Buriedness To Improve Discrimination between Actives and Inactives in Docking. - Noel M. O'Boyle; Suzanne Clare Brewerton; Robin Taylor (J. Chem. Inf. Model., 2008)

Testing Assumptions and Hypotheses for Rescoring Success in Protein-Ligand Docking. - Noel M. O'Boyle; John W. Liebeschuetz; Jason C. Cole (J. Chem. Inf. Model., 2009)

Review of "Data Analysis with Open Source Tools" by Philipp K Janert. - Noel M. O'Boyle (J. Cheminformatics, 2011)

Open Babel: An open chemical toolbox. - Noel M. O'Boyle; Michael Banck; Craig A. James; Chris Morley; Tim Vandermeersch; Geoffrey R. Hutchison (J. Cheminformatics, 2011)

De novo design of molecular wires with optimal properties for solar energy conversion. - Noel M. O'Boyle; Casey M. Campbell; Geoffrey R. Hutchison (J. Cheminformatics, 2011)

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. - Noel M. O'Boyle; Rajarshi Guha; Egon L. Willighagen; Sam E. Adams; Jonathan Alvarsson; Jean-Claude Bradley; Igor V. Filippov; Robert M. Hanson; Marcus D. Hanwell; Geoffrey R. Hutchison; Craig A. James; Nina Jeliazkova; et al. (J. Cheminformatics, 2011)

Confab - Systematic generation of diverse low-energy conformers. - Noel M. O'Boyle; Tim Vandermeersch; Christopher J. Flynn; Anita R. Maguire; Geoffrey R. Hutchison (J. Cheminformatics, 2011)

Confab - generation of diverse low energy conformers. - Noel M. O'Boyle; Tim Vandermeersch; Geoffrey R. Hutchison (J. Cheminformatics, 2011)

Cheminformatics. - Jörg K. Wegner; Aaron D. Sterling; Rajarshi Guha; Andreas Bender 002; Jean-Loup Faulon; Janna Hastings; Noel M. O'Boyle; John P. Overington; Herman van Vlijmen; Egon L. Willighagen (Commun. ACM, 2012)

Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI. - Noel M. O'Boyle (J. Cheminformatics, 2012)

What compound should I make next? Using Matched Molecular Series for prospective medicinal chemistry. - Noel M. O'Boyle; Roger A. Sayle; Jonas Boström (J. Cheminformatics, 2014)

Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall. - Daniel M. Lowe; Noel M. O'Boyle; Roger A. Sayle (Database J. Biol. Databases Curation, 2016)

Comparing structural fingerprints using a literature-based similarity benchmark. - Noel M. O'Boyle; Roger A. Sayle (J. Cheminformatics, 2016)

Comparison of structure- and ligand-based scoring functions for deep generative models: a GPCR case study. - Morgan C. Thomas; Robert T. Smith; Noel M. O'Boyle; Chris de Graaf; Andreas Bender 002 (J. Cheminformatics, 2021)

Re-evaluating sample efficiency in de novo molecule generation. - Morgan C. Thomas; Noel M. O'Boyle; Andreas Bender 002; Chris de Graaf (CoRR, 2022)

Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation. - Morgan C. Thomas; Noel M. O'Boyle; Andreas Bender 002; Chris de Graaf (J. Cheminformatics, 2022)

Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential. - Sonja Peter; Lydia Siragusa; Morgan Thomas; Tommaso Palomba; Simon Cross; Noel M. O'Boyle; Dávid Bajusz; György G. Ferenczy; György M. Keserü; Giovanni Bottegoni; Brian Joseph Bender; I-Jen Chen; et al. (J. Chem. Inf. Model., 2024)

MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design. - Morgan C. Thomas; Noel M. O'Boyle; Andreas Bender 002; Chris de Graaf (J. Cheminformatics, 2024)

Chemical classification program synthesis using generative artificial intelligence. - Christopher J. Mungall; Adnan Malik; Daniel R. Korn; Justin T. Reese; Noel M. O'Boyle; Janna Hastings (CoRR, 2025)