Val Gillet
Professor of Chemoinformatics
Computational Information Systems Research Group,
Department of Information Studies
University of Sheffield
Phone: 0114 2222 652
Fax: 0114 278 0300
Email: v.gillet@sheffield.ac.uk.

NEWS: PhD Studentship Available

A PhD studentship is available to start in Oct 2009 fully funded by EPSRC and in collaboration with AstraZeneca. The project will investigate the application of new data analysis techniques to chemical databases with the aim of identifying novel bioactive compounds for drug discovery. EPSRC eligibility rules apply.

My Research Interests:

I head the Chemoinformatics section of the Computational Information Systems Research Group. My research interests are chemoinformatics and computational approaches to drug design including: combinatorial library design and diversity analysis; the development of novel molecular descriptors for similarity searching; the application of evolutionary algorithms to computational chemistry; the identification of structure-activity relationships; and structure-based drug design. I have a particular interest in machine learning approaches and applications of evolutionary algorithms.

Current Group Members:

Post-doctoral Researchers

  • Muhammad Alkarouri is a post-doc working on an EPSRC funded project on Array Design in collaboration with GlaxoSmithKline.
  • Eleanor Gardiner is a post-doc working on pharmacophore elucidation funded by Cambridge Crystallographic Data Centre.

KTP Associate

  • Iain Mott is a KTP Associate funded by Novartis Pharmaceuticals and the DTI working on applications of multiobjective optimisation to protein-ligand docking.

PhD Students

  • Daniel Butler is working in the area of 3D similarity searching
  • Richard Martin is a PhD student working on Application of Multi-resolution Approaches to the Representation of Small Molecules. Richard is funded by BBSRC and GlaxoSmithKline and is jointly supervised by Eleanor Gardiner. Richard won Best Oral Presentation at the recent Young Modellers Forum in London, 2008.
  • Hina Patel is a PhD student working on the Development of a De Novo Design Tool. Hina is jointly supervised by Dr. Beining Chen in the Department of Chemistry. Funded by EPSRC and Eli Lilly. Hina won Best Oral Presentation at the Young Modellers Forum in London, 2007 and CINF-IO Informatics Scholarship for Scientific Excellence at the American Chemical Society Meeting, New Orleans, , April 2008.
  • Georgios Papadatos is a PhD student working in the area of Data Mining for Lead Optimisation George is funded by EPSRC and GlaxoSmithKline.
  • Richard Sherhod is a PhD student working on Toxicity Prediction and is funded by Lhasa Limited.

Previous Group Members:

  • Kris Birchall completed his PhD on the Development of Novel Chemoinformatics Methods for Molecuar Similarity and Diversity Analyses in 2007. Kris was funded by BBSRC and GlaxoSmithKline.
  • Tummala Rama Krishna Reddy completed his PhD on the Identification of Therapeutic Leads for Prion Diseases in March 2007. Reddy’s project was jointly supervised by Dr. Beining Chen in the Department of Chemistry.
  • Kirstin Moffat completed her PhD in 2006 on The Development of Computational Methods for 3D Similarity and Structure-Based Design Techniques in Lead Optimisation. Funded by EPSRC and GlaxoSmithKline.
  • Illy Khatib and Orazio Nicolotti who both worked on The Application of Evolutionary Computing to Drug Design. This project was joint with Peter Fleming in Automatic Control and Systems Engineering at Sheffield and was funded by GlaxoSmithKline.
  • Sally Mardikian completed her PhD on Applications of Multiobjective Evolutionary Algorithms in problems in Bioinformatics in 2008. Sally was funded by the MRC and was a joint student with Dr. Dave Westhead and Dr. Richard Jackson at the University of Leeds.
  • Yogi Patel: Comparison of Pharmacophore Detection Programs. This project began as an MSc dissertation project carried out at GlaxoSmithKline. Yogi Patel completed his PhD on Searching and Clustering Pharmacological Fingerprints in 2008. Funded by Janssen Pharmaceuticals
  • Trudi Wright completed her PhD in 2004: Methods for Focussed Combinatorial Library Design, Funded by BBSRC and GlaxoSmithKline
  • Ed Barker completed his PhD in 2004: Development of Reduced Graphs as Novel Descriptors for Identifying Structure-Activity Relationships. Funded by EPSRC and AstraZeneca.
  • Simon Cottrell completed his PhD on the Alignment of Multiple Flexible Molecules in 2005. Funded by EPSRC with additional support from the Cambridge Crystallographic Data Centre.
  • Martin Whittle was a post doc funded by Pfizer UK working on Mining Molecular Bioassay Data. This project was joint with Peter Willett and finished in Dec 2004.
  • David Wilton was a post doc funded by Pfizer US working on Support Tools for Pharmacophore Identification. This project was joint with Peter Willett and finished inApril 2005.

Teaching Interests:

I am Programme Coordinator of the MSc(Res) in Chemoinformatics. The programme was the first of its kind to be set up world-wide back in 2000. Students on the programme learn skills in computing and information management and apply their skills to real-world chemical problems using state-of-the-art commercial software. The programme is supported by the pharmaceutical, agrochemical and chemical software industries through industrial placement projects.

 

Recent Publications:

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

Journal Articles

  • 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. In Press.
  • 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. In the Press.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Gardiner, E.J.; Gillet, V.J.; Willett, P & Cosgrove, D.A. Cluster Representation Using Reduced Graphs. Journal of Chemical Information and Modeling.47, 2007, 354-366.
  • 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.
  • 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: Theory and Simulation. Journal of Chemical Information and Modeling. 46, 2006, 2206-2219. DOI: 10.1021/ci0496144.
  • 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.
  • 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..
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Gillet, V.J., Willett, P., Bradshaw, J. Similarity Searching Using Reduced Graphs. Journal of Chemical Information and Computer Sciences 43, 2003, 338-345.
  • Patel, Y., Gillet, V.J., Bravi, G., Leach, A. 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: 371-380, 2002.
  • 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: 5069-5080, 2002.
  • 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: 375-385, 2002.
  • Gillet, V.J., Willett, P. Fleming, P.J., Green, D.V.S. Designing Focused Libraries Using MoSELECT. Journal of Molecular Graphics and Modelling. 20: 491-498, 2002.
  • 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: 835-857, 2001
  • 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: 841-859, 2001
  • 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: 265-287, 2000
  • 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: 295-307, 2000
  • 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: 169-177, 1999
  • 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: 165-179, 1998
  • 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: 731-740, 1997
  • 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: 34-50, 1995.