Biography

Following a degree in Chemistry from NUI Galway, Noel O'Boyle undertook a PhD in Computational Chemistry with Prof. Han Vos in Dublin City University. This was on the topic of "Surface Studies and Density Functional Theory Analysis of Ruthenium Polypyridyl Complexes". Moving into the field of cheminformatics for drug design, he took up a postdoctoral position with Prof Ciaran Regan, University College Dublin, where he contributed to several projects in the field of neurotherapeutics. He carried out further postdoctoral work with Dr John Mitchell, Unilever Centre for Molecular Informatics, University of Cambridge on protein similarity and feature selection in QSAR. Following this, as part of postdoctoral work at the Cambridge Crystallographic Data Centre, he worked on the protein-ligand docking software GOLD. He joined UCC in Sept 2009, when he was awarded a Health Research Board Career Development Fellowship to work on software for pharmacophore discovery.

Research Interests

Cheminformatics:

• Development and application of software for pharmacophore discovery and searching
• Improved scoring functions for protein-ligand docking
• Development and application of cheminformatics toolkits (OpenBabel, Cinfony)

Computational chemistry:

• Computational design of molecules with desired electronic properties

Links

Personal Website with more details on research interests.
Blog on cheminformatics, and applying web technologies to chemistry.

Publications

1. Testing assumptions and hypotheses for rescoring success in protein-ligand docking. N. M. O'Boyle, J. W. Liebeschuetz and J. C. Cole. J. Chem. Inf. Model. 2009, 49, 1871-1878. [Link]
2. Curcumin-induced degradation of PKCd is associated with enhanced dentate NCAM PSA expression and spatial learning in adult and aged Wistar rats. L. Conboy, A. G. Foley, N. M. O'Boyle, M. Lawlor, H. C. Gallagher, K. J. Murphy and C. M. Regan. Biochem. Pharm. 2009, 77, 1254-1265. [Link]
3. Cinfony - combining Open Source cheminformatics toolkits behind a common interface. N. M. O'Boyle and G. R. Hutchison. Chem. Cent. J. 2008, 2, 24. [Link]
4. Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction. N. M. O'Boyle, D. S. Palmer, F. Nigsch and J. B. O. Mitchell. Chem. Cent. J. 2008, 2, 21. [Link]
5. Using buriedness to improve discrimination between actives and inactives in docking. N. M. O'Boyle, S. C. Brewerton and R. Taylor. J. Chem. Inf. Model. 2008, 48, 1269-1278. [Link]
6. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. N. M. O'Boyle, C. Morley and G. R. Hutchison. Chem. Cent. J. 2008, 2, 5. [Link]
7. cclib: A library for package-independent computational chemistry algorithms. N. M. O'Boyle, A. L. Tenderholt and K. M. Langner. J. Comp. Chem. 2008, 29, 839-845. [Link]
8. A density functional theory study of the electronic properties of Os(II) and Os(III) complexes immobilized on Au(111). N. M. O'Boyle, T. Albrecht, D. H. Murgida, L. Cassidy, J. Ulstrup and J. G. Vos. Inorg. Chem. 2007, 46, 117-124. [Link]
9. Userscripts for the life sciences. E. L. Willighagen, N. M. O'Boyle, H. Gopalakrishnan, D. Jiao, R. Guha, C. Steinbeck and D. J. Wild. BMC Bioinformatcs. 2007, 8, 487. [Link]
10. Random Forest Models To Predict Aqueous Solubility. D. S. Palmer, N. M. O'Boyle, R. C. Glen and J. B. O. Mitchell. J. Chem. Inf. Model. 2007, 47, 150-158. [Link]
11. Using Reaction Mechanism to Measure Enzyme Similarity. N. M. O'Boyle, G. L. Holliday, D. E. Almonacid and J. B. O. Mitchell. J. Mol. Biol. 2007, 368, 1484-1499. [Link]
12. Probing inter-ligand excited state interaction in homo and heteroleptic ruthenium(II) polypyridyl complexes using selective deuteriation. W. R. Browne, P. Passanati, M. T. Gandolfi, R. Ballardini, W. Henry, A. Guckian, N. M. O'Boyle, J. J. McGarvey and J. G. Vos. Inorg. Chim. Acta. 2007, 360, 1183-1190. [Link]
13. MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. G. L. Holliday, D. E. Almonacid, G. J. Bartlett, N. M. O'Boyle, J. W. Torrance, P. Murray-Rust, J. B. O. Mitchell and J. M. Thornton. Nucleic Acid Res. 2007, 35, D515-D520. [Link]
14. PYCHEM: a multivariate analysis package for python. R. M. Jarvis, D. Broadhurst, H. Johnson, N. M. O'Boyle and R. Goodacre. Bioinformatics. 2006, 22, 2565-2566. [Link]
15. MACiE: a database of enzyme reaction mechanisms. G. L. Holliday, G. J. Bartlett, D. E. Almonacid, N. M. O'Boyle, P. Murray-Rust, J. M. Thornton and J. B. O. Mitchell. Bioinformatics. 2005, 21, 4315-4316. [Link]
16. Ground vs. excited state interaction in ruthenium-thienyl dyads: implications for through bond interactions in multicomponent systems. W. Henry, W. R. Browne, K. L. Ronayne, N. M. O'Boyle, J. G. Vos and J. J. McGarvey. J. Mol. Struct. 2005, 735-736, 123-134. [Link]
17. Ground- and Excited-State Electronic Structure of an Emissive Pyrazine-Bridged Ruthenium(II) Dinuclear Complex. W. R. Browne, N. M. O'Boyle, W. Henry, A. L. Guckian, S. Horn, T. Fett, C. M. O'Connor, M. Duati, L. De Cola, C. G. Coates, K. L. Ronayne, J. J. McGarvey and J. G. Vos. J. Am. Chem. Soc. 2005, 127, 1229-1241. [Link]
18. Accessing the CDK using Python. N. M. O'Boyle. CDK News. 2005, 2, 40-42.
19. Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems. W. R. Browne, N. M. O'Boyle, J. J. McGarvey and J. G. Vos. Chem. Soc. Rev. 2005, 34, 641-663. [Link]
20. Synthesis and characterisation of ruthenium complexes containing a pendent catechol ring. L. O'Brien, M. Duati, S. Rau, A. L. Guckian, T. E. Keyes, N. M. O'Boyle, A. Serr, H. Gorls and J. G. Vos. Dalton Trans. 2004, 514-522. [Link]
21. Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes. A. L. Guckian, M. Doering, M. Ciesielski, O. Walter, J. Hjelm, N. M. O'Boyle, W. Henry, W. R. Browne, J. J. McGarvey and J. G. Vos. Dalton Trans. 2004, 3943-3949. [Link]