The University of Sheffield
Information School

Professor Val Gillet

Professor of Chemoinformatics, Head of School

MA (Cambridge); MSc (Sheffield); PhD (Sheffield)

Val Gillet Room number: 305
Telephone (internal): 22652
Telephone (UK): 0114 222 2652
Telephone (International): +44 114 222 2652
Email: v.gillet@sheffield.ac.uk

After completing a degree in Natural Sciences at Cambridge, I took a short term research post in the Department of Information Studies (as the Information School was then called) and contributed to the building of a database of generic chemical structures as found in the patent literature. This post fueled my interest in computing and I took the MSc in Information Science, returning to the generic structures project for my master’s dissertation and subsequent PhD - this time developing novel search algorithms to retrieve structural information from the database. I then moved to the Chemistry Department at Leeds University where I led a team working on de novo design (that is, the in-silico design of chemical compounds to fit a set of constraints such as a protein binding site) before returning to Sheffield in the mid-nineties and taking up an academic post.

Teaching

My teaching interests are in applied computational techniques, especially to problems involving chemical structures; a field which has become known as Chemoinformatics. While chemoinformatics can be broadly defined as the manipulation and analysis of chemical information, my particular interest is in the analysis of structural information with application to drug design. I teach an introductory class to first year undergraduates and also post-graduate modules to masters and PhD students. In addition, I organise and run an annual short course which provides a practical introduction to chemoinformatics and which attracts PhD students from around Europe alongside delegates from industry.

Professional standing

Research interests

Chemoinformatics in particular: data mining and machine learning methods; virtual screening; structure-activity relationships; de novo design; and evolutionary algorithms.

Key publications

Book

Leach A.R., Gillet V.J. An Introduction to Chemoinformatics, Revised Edition, Springer, 2007.

Journal Articles

Taylor, R., Cole, J.C., Cosgrove, D.A., Gardiner, E.J. Gillet, V.J. Development and Validation of an Improved Algorithm for Overlaying Flexible Molecules. Journal of Computer-Aided Molecular Design. In Press.

Martin, R.L., Gardiner, E., Gillet, V.J., Senger, S. Compression of Molecular Interaction Fields using Wavelets Thumbnails: Application to Molecular Alignment. Journal of Chemical Information and Modelling. 52, 2012, 757-769. DOI: 10.1021/ci200348h.

Papadatos, G., Alkarouri, M., Gillet, V.J., Willett, P., Kadirkamanathan, V., Luscombe, C.N., Bravi, G., Richmond, N.J., Pickett, S.D., Hussain, J., Pritchard, J.M., Cooper, A.W.J., Macdonald S.J.F. Lead Optimisation Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility and Lipophilicity. Journal of Chemical Information and Modelling. 50, 2010, 1872-1886. DOI: 10.1021/ci100258p

Martin, R.L.; Gardiner, E.; Gillet, V.J.; Munoz-Muriedas, J. & Senger, S. Wavelet Approximation of GRID Fields: Application to Quantitative Structure-Activity Relationships. Molecular Informatics, 29, 2010, 603-620. DOI: 10.1002/minf.201000066.

Papadatos, G.; Alkarouri, M.; Gillet, V.J.; Willett, P.; Kadirkamanathan, V.; Luscombe, C.N.; Bravi, G.; Richmond, N.J.; Pickett, S.D.; Hussain, J.; Pritchard, J.M.; Cooper, A.W.J.; Macdonald, S.J.F. Lead Optimization Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility, and Lipophilicity. Journal of Chemical Information and Modeling, 50, 2010, 1872-1886. DOI: 10.1021/ci100258p

Leach, A.R.; Gillet, V.J.; Lewis, R.A. & Taylor, R. Three-Dimensional Pharmacophore Methods in Drug Discovery. Journal of Medicinal Chemistry, 53, 2010, 539-558. DOI: 10.1021/jm900817u

Gardiner, E.J.; Gillet V.J.; Cosgrove D. & Taylor R. Multiobjective Optimisation of Pharmacophore Hypotheses: Bias Towards Low-Energy Conformations. Journal of Chemical Information and Modelling, 49, 2009, 2761-2773. DOI: 10.1021/ci9002816

Birchall, K.; Gillet, V.J.; Willett, P.; Ducrot, P. & Lutteman C. Use of Reduced Graphs to Encode Bioisosterism for Similarity-Based Virtual Screening. Journal of Chemical Information and Modelling, 49, 2009, 1330-1346. DOI: 10.1021/ci900078h

Patel, H.; Chen, B.; Gillet V.J. & Bodkin, M.J. Knowledge-Based Approach to De Novo Design Using Reaction Vectors. Journal of Chemical Information and Modeling, 49, 2009, 1163-1184. DOI: 10.1021/ci800413m

Gardiner, E.J.; Gillet, V.J.; Haranczyk, M.; Hert, J.; Holliday, J.D.; Malim, N.; Patel Y. & Willett , P. Turbo Similarity Searching: Effect of Fingerprint and Dataset on Virtual-Screening Performance. Statistical Analysis and Data Mining, 2, 2009, 103-114.

Papadatos, G.; Cooper, A.W.J.; Kadirkamanathan, K.; MacDonald, S.J.F.; McLay, I.M.; Pickett, S.D.; Pritchard, J.M.; Willett, P. & Gillet, V.J., Analysis of Neighbourhood Behaviour in Lead Optimisation and Array Design. Journal of Chemical Information and Modeling, 49, 2009, 195-208. DOI: 10.1021/ci800302g

Patel, Y.; Gillet, V.J.; Howe, T.; Pastor, J.; Oyarzabal, J. & Willett, P. Assessment of Additive/Non-Additive Effects in Structure-Activity Relationships: Implications for Iterative Drug Design. Journal of Medicinal Chemistry, 51, 2008, 7552-7562. DOI: 10.1021/jm801070q

Birchall, K.; Gillet, V.J.; Harper, G. & Pickett, S.D. Evolving Interpretable Structure-Activity Relationship Models. Part 1: Reduced Graph Queries. Journal of Chemical Information and Modeling 48, 2008, 1543-1557. DOI: 10.1021/ci8000502

Birchall, K.; Gillet, V.J.; Harper, G. & Pickett, S.D. Evolving Interpretable Structure-Activity Relationship Models. Part 2: Using Multiobjective Optimisation to Derive Multiple Models. Journal of Chemical Information and Modeling, 48, 2008, 1558-1570. DOI: 10.1021/ci800051h

Moffat, K.M.; Gillet, V.J.; Bravi, G. & Leach A.R. A Comparison of Field-Based Similarity Methods. Journal of Chemical Information and Modeling, 48, 2008, 719-729. DOI: 10.1021/ci700130j

Gillet, V.J. New Directions in Library Design and Analysis. Current Opinion in Chemical Biology, 12, 2008, 372-378 DOI: 10.1016/j.cbpa.2008.02.015

Whittle M.; Eaglestone B.; Ford N.; Gillet V.J. & Madden A. Data Mining of Search Engine Logs. Journal of the American Society for Information Science and Technology, 58, 2007, 2382-2400. DOI: 10.1002/asi.20733

Gardiner, E.J.; Gillet, V.J.; Willett, P & Cosgrove, D.A. Representing Clusters Using a Maximum Common Edge Substructure Algorithm Applied to Reduced Graphs and Molecular Graphs. Journal of Chemical Information and Modeling, 47, 2007, 354-366. DOI: 10.1021/ci600444g

Cottrell, S.J.; Gillet, V.J. & Taylor, R. Incorporating Partial Matches within Multiobjective Pharmacophore Identification. Journal of Computer-Aided Molecular Design, 20, 2006, 735-749. DOI: 10.1007/s10822-006-9086-7

Whittle M.; Eaglestone B.; Ford N.; Gillet V.J. & Madden A., Query Transformations and their Role in Web Searching by the General Public. Information Research, 12, 2006.

Whittle, M.; Gillet, V.J.; Willett, P.; Alex, A. & Loesel, J. Analysis of Data Fusion Methods in Virtual Screening: Similarity and Group Fusion. Journal of Chemical Information and Modeling, 46, 2006, 2193-2205. DOI: 10.1021/ci0496144

Whittle, M.; Gillet, V.J.; Willett, P.; Alex, A. & Loesel, J. Analysis of Data Fusion Methods in Virtual Screening: Theoretical Model. Journal of Chemical Information and Modeling, 46, 2006, 2206-2219. DOI: 10.1021/ci049615w

Ganguly, M.,; Brown, N.; Schuffenhauer, A; Ertl, P.; Gillet, V.J. & Greenidge, P. Introducing the Consensus Modeling Concept in Genetic Algorithms: Application to Interpretable Discriminant Analysis. Journal of Chemical Information and Modeling, 46, 2006, 2110-2124. DOI: 10.1021/ci0505291

Birchall, K, Gillet, V.J., Harper, G. & Pickett, S.D. Training Similarity Searches for Specific Activities: Application to Reduced Graphs. Journal of Chemical Information and Modeling, 46, 2006, 577-586. DOI: 10.1021/ci050465e

Barker E.; Buttar, D.; Cosgrove, D.; Gardiner, E.; Willett, P. & Gillet, V.J. Scaffold Hopping Using Clique Detection Applied to Reduced Graphs. Journal of Chemical Information and Modeling, 46, 2006, 503-511. DOI: 10.1021/ci050347r

Reddy, T.R.K.; Mutter, R.; Heal, W.; Guo, K.; Gillet, V.J.; Pratt, S. & Chen B. Library Design, Synthesis, and Screening: Pyridine Dicarbonitriles as Potential Prion Disease Therapeutics. Journal of Medicinal Chemistry, 49, 2006, 607-615. DOI: 10.1021/jm050610f

Kristam, R.; Gillet, V.J.; Lewis, R.A. & Thorner, D. Comparison of Conformational Analysis Techniques to Generate Pharmacophore Hypotheses Using Catalyst. Journal of Chemical Information and Modeling, 45, 2005, 461-476. DOI: 10.1021/ci049731z

Cottrell, S.; Gillet, V.J.; Taylor R. & Wilton, D. Generation of Multiple Pharmacophore Hypotheses Using Multiobjective Optimisation Techniques. Journal of Computer-Aided Molecular Design, 18, 2004, 665-682. DOI: 10.1007/s10822-004-5523-7

Whittle, M.; Gillet, V.J.; Willett, P.; Alex, A. & Loesel, J. Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients. Journal of Chemical Information and Computer Sciences, 44, 2004, 1840-1848. DOI: 10.1021/ci049867x

Gillet, V.J. Applications of Evolutionary Computation in Drug Design. Applications of Evolutionary Computation in Chemistry, 110, 2004, 133-152. DOI: 10.1007/b13935

Wright, T.; Gillet, V.J.; Green, D.V.S. & Pickett, S.D. Optimising the Size and Configuration of Combinatorial Libraries. Journal of Chemical Information and Computer Sciences, 43, 2003, 381-390. DOI: 10.1021/ci0255836

Barker, E.; Gardiner, E.; Gillet, V.J.; Kitts, P. & Morris, J. Further Development of Reduced Graphs for Identifying Bioactive Compounds. Journal of Chemical Information and Computer Sciences, 43, 2003, 346-356. DOI: 10.1021/ci0255937

Gillet, V.J.; Willett, P. & Bradshaw, J. Similarity Searching Using Reduced Graphs. Journal of Chemical Information and Computer Sciences, 43, 2003, 338-345. DOI: 10.1021/ci025592e

Bishop, N.; Gillet, V.J.; Holliday, J.D. & Willett, P. Chemoinformatics Research at the University of Sheffield: a History and Citation Analysis. Journal of Information Science, 29, 2003, 249-267.

Patel, Y.; Gillet, V.J.; Bravi, G. & Leach, A.R. A Comparison of the Pharmacophore Identification Programs: Catalyst, DISCO and GASP. Journal of Computer-Aided Molecular Design, 16, 2002, 693-681.

Gillet, V.J. Reactant- and Product-Based Approaches to the Design of Combinatorial Libraries. Journal of Computer-Aided Molecular Design, 16, 2002, 371-380.

Nicolotti, O.; Gillet, V.J.; Fleming, P.J. & Green, D.V.S. Multiobjective Optimisation in Quantitative Structure-Activity Relationships: Deriving Accurate and Interpretable QSARs. Journal of Medicinal Chemistry, 45, 2002, 5069-5080. DOI: 10.1021/jm020919o

Gillet, V.J.; Khatib, W.; Willett, P.; Fleming, P.J. & Green, D.V.S. Combinatorial Library Design Using a Multiobjective Genetic Algorithm. Journal of Chemical Information and Computer Sciences, 42, 2002, 375-385. DOI: 10.1021/ci010375j

Gillet, V.J.; Willett, P.; Fleming, P.J. & Green, D.V.S. Designing Focused Libraries Using MoSELECT. Journal of Molecular Graphics and Modelling. 20, 2002, 491-498.

Watson, P.; Willett, P.; Gillet, V.J. & Verdonk, M.L. Calculating the Knowledge-based Similarity of Functional Groups Using Crystallographic Data. Journal of Computer-Aided Molecular Design, 15, 2001, 835-857.

Verdonk, M.L.; Cole, J.C.; Watson, P.; Gillet, V.J. & Willett, P. SuperStar: Improved Knowledge-Based Interaction Fields for Protein Binding Sites. Journal of Molecular Biology, 307, 2001, 841-859.

Gillet, V.J. & Nicolotti, O. Evaluation of Reactant-Based and Product-Based Approaches to the Design of Combinatorial Libraries. Perspectives in Drug Discovery and Design, 20, 2000, 265-287.

Schuffenhauer, A.; Gillet, V.J. & Willett, P. Similarity Searching in Files of 3D Chemical Structures: Analysis of the BIOSTER Database Using 2D Fingerprints and Molecular Field Descriptors. Journal of Chemical Information and Computer Sciences, 40, 2000, 295-307.

Gillet, V.J.; Willett, P.; Bradshaw, J. & Green, D.V.S. Selecting Combinatorial Libraries to Optimise Diversity and Physical Properties. Journal of Chemical Information and Computer Sciences, 39, 1999, 169-177.

Gillet, V.J.; Willett, P. & Bradshaw, J. Identification Of Biological Activity Profiles Using Substructural Analysis And Genetic Algorithms. Journal of Chemical Information and Computer Sciences, 38, 1998, 165-179.

Gillet, V.J.; Willett, P. & Bradshaw, J. The Effectiveness of Reactant Pools for Generating Structurally Diverse Combinatorial Libraries. Journal of Chemical Information and Computer Sciences, 37, 1997, 731-740.

Gillet, V.J.; Myatt, G.; Zsoldos, Z. & Johnson, A. P. SPROUT, HIPPO and CAESAR: Tools for De Novo Structure Generation Using Templates. Perspectives in Drug Discovery and Design, 3, 1995, 34-50.