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4. Noel O'Boyle

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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 (Open Babel, Cinfony)

Computational chemistry:

• Computational design of molecules with desired electronic properties

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Publications

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Edited Books

	Year	Publication
	(2011)	Noel M O'Boyle (Ed.). (2011) Open Babel - Official User Guide. Raleigh: Lulu Press, Inc.   [Details]

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Peer Reviewed Journals

	Year	Publication
	(2011)	'Computational Design and Selection of Optimal Organic Photovoltaic Materials' O'Boyle, NM,Campbell, CM,Hutchison, GR; (2011) 'Computational Design and Selection of Optimal Organic Photovoltaic Materials' [DOI] [CORA Link] [Details]
	(2011)	'Open Babel: An open chemical toolbox' O'Boyle, NM; Banck, M; James, CA; Morley, C; Vandermeersch, T; Hutchison, GR (2011) 'Open Babel: An open chemical toolbox' Chemistry Central   [DOI] [CORA Link] [Details]
	(2011)	'Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on' O'Boyle, NM; Guha, R; Willighagen, EL; Adams, SE; Alvarsson, J; Bradley, JC; Filippov, IV; Hanson, RM; Hanwell, MD; Hutchison, GR; James, CA; Jeliazkova, N; Lang, ASID; Langner, KM; Lonie, DC; Lowe, DM; Pansanel, J; Pavlov, D; Spjuth, O; Steinbeck, C; Tenderholt, AL; Theisen, KJ; Murray-Rust, P (2011) 'Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on' Chemistry Central   [DOI] [CORA Link] [Details]
	(2011)	'Confab - Systematic generation of diverse low-energy conformers' O'Boyle NM, Vandermeersch T, Flynn CJ, Maguire AR, Hutchison GR; (2011) 'Confab - Systematic generation of diverse low-energy conformers'   [DOI] [CORA Link] [Details]
	(2009)	'Testing Assumptions and Hypotheses for Rescoring Success in Protein-Ligand Docking' O'Boyle, Noel M. and Liebeschuetz, John W. and Cole, Jason C.; (2009) 'Testing Assumptions and Hypotheses for Rescoring Success in Protein-Ligand Docking' [DOI] [Details]
	(2009)	'Curcumin-induced degradation of PKC delta is associated with enhanced dentate NCAM PSA expression and spatial learning in adult and aged Wistar rats' Conboy, Lisa and Foley, Andrew G. and O'Boyle, Noel M. and Lawlor, Marie and Gallagher, Helen C. and Murphy, Keith J. and Regan, Ciaran M.; (2009) 'Curcumin-induced degradation of PKC delta is associated with enhanced dentate NCAM PSA expression and spatial learning in adult and aged Wistar rats' [DOI] [Details]
	(2008)	'Cinfony - combining Open Source cheminformatics toolkits behind a common interface' O'Boyle, Noel M. and Hutchison, Geoffrey R.; (2008) 'Cinfony - combining Open Source cheminformatics toolkits behind a common interface' [DOI] [Details]
	(2008)	'Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction' O'Boyle, Noel M. and Palmer, David S. and Nigsch, Florian and Mitchell, John B. O.; (2008) 'Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction' [DOI] [Details]
	(2008)	'Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit' O'Boyle, Noel M. and Morley, Chris and Hutchison, Geoffrey R.; (2008) 'Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit' [DOI] [Details]
	(2008)	'Using buriedness to improve discrimination between actives and inactives in docking' O'Boyle, Noel M. and Brewerton, Suzanne C. and Taylor, Robin; (2008) 'Using buriedness to improve discrimination between actives and inactives in docking' [DOI] [Details]
	(2008)	'cclib: A library for package-independent computational chemistry algorithms' O'Boyle, Noel M. and Tenderholt, Adam L. and Langner, Karol M.; (2008) 'cclib: A library for package-independent computational chemistry algorithms' [DOI] [Details]
	(2007)	'Userscripts for the life sciences' Willighagen, Egon L. and O'Boyle, Noel M. and Gopalakrishnan, Harini and Jiao, Dazhi and Guha, Rajarshi and Steinbeck, Christoph and Wild, David J.; (2007) 'Userscripts for the life sciences' [DOI] [Details]
	(2007)	'Using reaction mechanism to measure enzyme similarity' O'Boyle, Noel M. and Holliday, Gemma L. and Almonacid, Daniel E. and Mitchell, John B. O.; (2007) 'Using reaction mechanism to measure enzyme similarity' [DOI] [Details]
	(2007)	'Probing inter-ligand excited state interaction in homo and heteroleptic ruthenium(II) polypyridyl complexes using selective deuteriation' Browne, Wesley R. and Passaniti, Paolo and Gandolfi, Maria Teresa and Ballardini, Roberto and Henry, William and Guckian, Adrian and O'Boyle, Noel and McGarvey, John J. and Vos, Johannes G.; (2007) 'Probing inter-ligand excited state interaction in homo and heteroleptic ruthenium(II) polypyridyl complexes using selective deuteriation' [DOI] [Details]
	(2007)	'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms' Holliday, Gemma L. and Almonacid, Daniel E. and Bartlett, Gail J. and O'Boyle, Noel M. and Torrance, James W. and Murray-Rust, Peter and Mitchell, John B. O. and Thornton, Janet M.; (2007) 'MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms' [DOI] [Details]
	(2007)	'Random forest models to predict aqueous solubility' Palmer, David S. and O'Boyle, Noel M. and Glen, Robert C. and Mitchell, John B. O.; (2007) 'Random forest models to predict aqueous solubility' [DOI] [Details]
	(2007)	'A density functional theory study of the electronic properties of Os(II) and Os(III) complexes immobilized on Au(111)' O'Boyle, Noel M. and Albrecht, Tim and Murgida, Daniel H. and Cassidy, Lynda and Ulstrup, Jens and Vos, Johannes G.; (2007) 'A density functional theory study of the electronic properties of Os(II) and Os(III) complexes immobilized on Au(111)' [DOI] [Details]
	(2006)	'PYCHEM: a multivariate analysis package for python' Jarvis, Roger M. and Broadhurst, David and Johnson, Helen and O'Boyle, Noel M. and Goodacre, Royston; (2006) 'PYCHEM: a multivariate analysis package for python' [DOI] [Details]
	(2005)	'MACiE: a database of enzyme reaction mechanisms' Holliday, GL and Bartlett, GJ and Almonacid, DE and O'Boyle, NM and Murray-Rust, P and Thornton, JM and Mitchell, JBO; (2005) 'MACiE: a database of enzyme reaction mechanisms' [DOI] [Details]
	(2005)	'Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems' Browne, WR and O'Boyle, NM and McGarvey, JJ and Vos, JG; (2005) 'Elucidating excited state electronic structure and intercomponent interactions in multicomponent and supramolecular systems' [DOI] [Details]
	(2005)	'Ground vs. excited state interaction in ruthenium-thienyl dyads: implications for through bond interactions in multicomponent systems' Henry, W and Browne, WR and Ronayne, KL and O'Boyle, NM and Vos, JG and McGarvey, JJ; (2005) 'Ground vs. excited state interaction in ruthenium-thienyl dyads: implications for through bond interactions in multicomponent systems' [DOI] [Details]
	(2005)	'Ground- and excited-state electronic structure of an emissive pyrazine-bridged Ruthenium(II) dinuclear complex' Browne, WR and O'Boyle, NM and Henry, W and Guckian, AL and Horn, S and Fett, T and O'Connor, CM and Duati, M and De Cola, L and Coates, CG and Ronayne, KL and McGarvey, JJ and Vos, JG; (2005) 'Ground- and excited-state electronic structure of an emissive pyrazine-bridged Ruthenium(II) dinuclear complex' [DOI] [Details]
	(2004)	'Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes' Guckian, AL and Doering, M and Ciesielski, M and Walter, O and Hjelm, J and O'Boyle, NM and Henry, W and Browne, WR and McGarvey, JJ and Vos, JG; (2004) 'Assessment of intercomponent interaction in phenylene bridged dinuclear ruthenium(II) and osmium(II) polypyridyl complexes' [DOI] [Details]
	(2004)	'Synthesis and characterisation of ruthenium complexes containing a pendent catechol ring' O'Brien, L and Duati, M and Rau, S and Guckian, AL and Keyes, TE and O'Boyle, NM and Serr, A and Gorls, H and Vos, JG; (2004) 'Synthesis and characterisation of ruthenium complexes containing a pendent catechol ring' [DOI] [Details]

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Conference Publications

	Year	Publication
	(2011)	5th Meeting on US Government Chemical Databases and Open Chemistry O'Boyle, NM (2011) Improving the quality of chemical databases with community-developed tools (and vice versa) 5th Meeting on US Government Chemical Databases and Open Chemistry Frederick (Maryland), US, , 25-AUG-11 - 26-AUG-11 [Details]
	(2011)	Visions of a Semantic Molecular Future - A symposium to celebrate the career of Peter Murray-Rust O'Boyle, NM (2011) The Blue Obelisk community Visions of a Semantic Molecular Future - A symposium to celebrate the career of Peter Murray-Rust Cambridge, UK, , 17-JAN-11 - 17-JAN-11 [Details]
	(2011)	Wellcome Trust Workshop on Molecular Informatics Open Source Software (MIOSS) O'Boyle, NM (2011) Cinfony - Bringing cheminformatics toolkits into tune Wellcome Trust Workshop on Molecular Informatics Open Source Software (MIOSS) Hinxton, UK, , 04-MAY-11 - 06-MAY-11 [Details]
	(2010)	6th German Conference on Chemoinformatics O'Boyle, NM; Campbell, CM; Hutchison, GR (2010) De novo design of molecular wires with optimal properties for solar energy conversion 6th German Conference on Chemoinformatics Goslar, Germany, , 07-NOV-10 - 09-NOV-10 [Details]
	(2010)	6th German Conference on Chemoinformatics O'Boyle, NM; Vandermeersch, T; Hutchison, GR (2010) Confab - Systematic generation of diverse low-energy conformers 6th German Conference on Chemoinformatics Goslar, Germany, , 07-NOV-10 - 09-NOV-10 [Details]
	(2010)	239th ACS National Meeting Geoffrey R Hutchison and Noel M O'Boyle; (2010) Organic electronic materials by design: Finding a needle through the haystack 239th ACS National Meeting San Francisco, US, , 21-MAR-10 - 25-MAR-10 [Details]
	(2010)	Gordon Research Conference on Electron Donor-Acceptor Interactions Geoffrey R Hutchison, Casey M Campbell and Noel M O'Boyle. ; (2010) Computational Design and Selection of Optimal Organic Photovoltaics Materials: Finding Needles Through the Haystack Gordon Research Conference on Electron Donor-Acceptor Interactions Newport (Rhode Island), US, , 08-AUG-10 - 13-AUG-10 [Details]
	(2010)	239th ACS National Meeting Noel M O'Boyle and Geoffrey R Hutchison; (2010) Cinfony - Combining disparate cheminformatics resources into a single toolkit 239th ACS National Meeting San Francisco, US, , 21-MAR-10 - 25-MAR-10 [Details]

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Conference Contributions

	Year	Publication
	(2010)	Symposium on Visual Analysis of Chemical Data at 239th ACS National Meeting, Noel M O'Boyle, Andrew SID Lang, Jean-Claude Bradley; (2010) Proposer, co-organiser and co-chair of a 3-session symposium with 23 oral contributions including one keynote. [Conference Organising Committee Member], Symposium on Visual Analysis of Chemical Data at 239th ACS National Meeting, San Francisco, US , 22-MAR-10 - 23-MAR-10

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Published Reports

	Year	Publication
	(2011)	Review of Data Analysis with Open Source Tools by Philipp K Janert. Noel M O'Boyle; (2011) Review of Data Analysis with Open Source Tools by Philipp K Janert. BioMedCentral, Journal of Cheminformatics.   [DOI] [Details]

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Professional Activities

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Honours and Awards

	Year	Title	Awarding Body
	2010	Jacques-Émile Dubois Grant	Chemical Structure Association Trust