Research Topics
| P WillettSummaryAffiliation: University of Sheffield Country: UK Publications
| Collaborators
|
Detail Information
Publications
Scaffold hopping using clique detection applied to reduced graphsEdward J Barker
Department of Information Studies and Krebs Institute for Biomolecular Research, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
J Chem Inf Model 46:503-11. 2006..We show that graph matching using fully connected reduced graphs is an effective retrieval method and that the actives retrieved are likely to be topologically different from those retrieved using conventional 2D methods...- The Journal of Computer-Aided Molecular Design: a bibliometric notePeter Willett
Information School, University of Sheffield, Sheffield, UK
J Comput Aided Mol Des 26:153-7. 2012..The citations to the journal come from almost 2000 different sources that span a very wide range of academic subjects, with the most heavily cited articles being descriptions of software systems and of computational methods... - A graph-theory method for pattern identification in geographical epidemiology--a preliminary application to deprivation and mortalityRavi Maheswaran
Public Health GIS Unit, School of Health and Related Research, University of Sheffield, Regent Court, 30 Regent Street, Sheffield S14DA, UK
Int J Health Geogr 8:28. 2009.... - Chemoinformatics - similarity and diversity in chemical librariesP Willett
Department of Information Studies, University of Sheffield, Sheffield, S10 2TN, UK
Curr Opin Biotechnol 11:85-8. 2000.... - Similarity-based approaches to virtual screeningP Willett
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
Biochem Soc Trans 31:603-6. 2003.... - Similarity-based virtual screening using 2D fingerprintsPeter Willett
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, 211 Portobello, Sheffield S1 4DP, UK
Drug Discov Today 11:1046-53. 2006..We demonstrate the effectiveness of this approach to screening, and also describe an approximate form of group fusion, turbo similarity searching, that can be used when just a single reference structure is available... - Prediction of ion channel activity using binary kernel discriminationPeter Willett
Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, United Kingdom
J Chem Inf Model 47:1961-6. 2007..The results obtained suggest that the approach provides an effective way of prioritizing compounds for acquisition and testing... - Searching techniques for databases of two- and three-dimensional chemical structuresPeter Willett
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield, UK
J Med Chem 48:4183-99. 2005 - Dissimilarity-based algorithms for selecting structurally diverse sets of compoundsP Willett
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, United Kingdom
J Comput Biol 6:447-57. 1999..Procedures are described for selecting a diverse subset of an entire database, and for selecting diverse combinatorial libraries using both reagent-based and product-based selection... - Evaluation of a Bayesian inference network for ligand-based virtual screeningBeining Chen
Krebs Institute for Biomolecular Research, Departments of Chemistry and of Information Studies, University of Sheffield, Sheffield, S10 2TN, UK
J Cheminform 1:5. 2009..Here, we modify the approach to enable a Bayesian inference network to be used for chemical similarity searching, where a database is ranked in order of decreasing probability of bioactivity... - Multiple search methods for similarity-based virtual screening: analysis of search overlap and precisionJohn D Holliday
Information School, University of Sheffield, Portobello Street, Sheffield S1 4DP, UK
J Cheminform 3:29. 2011..abstract:.. - A bibliometric analysis of the Journal of Molecular Graphics and ModellingPeter Willett
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, UK
J Mol Graph Model 26:602-6. 2007..The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported... - Identification of biological activity profiles using substructural analysis and genetic algorithmsV J Gillet
Department of Information Studies, University of Sheffield, Western Bank, United Kingdom
J Chem Inf Comput Sci 38:165-79. 1998..The effectiveness of the approach is further increased by using a genetic algorithm for the calculation of the weights comprising a profile. The methods have been successfully applied to a number of different data sets... - Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA)D B Turner
Krebs Institute for Biomolecular Research, University of Sheffield, U K
J Comput Aided Mol Des 14:1-21. 2000.... - Virtual screening using binary kernel discrimination: effect of noisy training data and the optimization of performanceBeining Chen
Department of Chemistry, University of Sheffield, Sheffield S10 2TN, UK
J Chem Inf Model 46:478-86. 2006.... - GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3DNicola J Richmond
Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, 211 Portobello St, Sheffield, S7 4DP, UK
J Comput Aided Mol Des 20:567-87. 2006.... - Automatic generation of alignments for 3D QSAR analysesN E Jewell
Department of Information Studies and Krebs Institute for Biomolecular Research, University of Sheffield, UK
J Mol Graph Model 20:111-21. 2001..The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments... - Use of graph theory to identify patterns of deprivation and high morbidity and mortality in public health data setsPeter A Bath
Centre for Health Information Management Research CHIMR, Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN UK
J Am Med Inform Assoc 12:630-41. 2005..More specifically, the study aimed to identify chains of EDs with high deprivation, morbidity, and mortality that might be adjacent to specific types of geographic features, i.e., rivers or major roads... - Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-stringsJ D Holliday
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, S10 2TN, UK
Comb Chem High Throughput Screen 5:155-66. 2002..The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems... - Searching for patterns of amino acids in 3D protein structuresRuth V Spriggs
Krebs Institute for Biomolecular Research and Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
J Chem Inf Comput Sci 43:412-21. 2003..The effectiveness of these approaches is demonstrated by extensive searches of the Protein Data Bank for typical 3D query patterns... - Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functionsChidochangu P Mpamhanga
Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
J Chem Inf Model 46:686-98. 2006..Principal component analysis and clustering of the fingerprints permits the easy separation of active from inactive binding modes and the visualization of diverse binding modes... - Genomic data analysis using DNA structure: an analysis of conserved nongenic sequences and ultraconserved elementsEleanor J Gardiner
Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
J Chem Inf Model 46:753-61. 2006..We have used Fourier techniques to analyze the UCEs and CNGs in terms of their octamer structural properties, to reveal structural correlations which may indicate possible functions for some of these sequences... - Representing clusters using a maximum common edge substructure algorithm applied to reduced graphs and molecular graphsEleanor J Gardiner
Department of Information Studies, University of Sheffield, 211 Portobello Street, Regent Court, Sheffield, United Kingdom
J Chem Inf Model 47:354-66. 2007..Clusters of interest are then subject to a detailed R-group analysis using the same iterated MCES algorithm applied to the molecular graphs... - A structural similarity analysis of double-helical DNAEleanor J Gardiner
Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
J Mol Biol 343:879-89. 2004.... - Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficientsMartin Whittle
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, U K
J Chem Inf Comput Sci 44:1840-8. 2004..The use of group recall can lead to improved enrichment in database searches and virtual screening... - Combinatorial library design using a multiobjective genetic algorithmValerie J Gillet
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
J Chem Inf Comput Sci 42:375-85. 2002..The library designer can then make an informed choice on which solution(s) to explore. Various performance characteristics of MoSELECT are reported based on a number of different combinatorial libraries... - Analysis of data fusion methods in virtual screening: theoretical modelMartin Whittle
Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, UK
J Chem Inf Model 46:2193-205. 2006..The model shows that two standard fusion rules can give performance enhancements in some cases but that the results of fusion are dependent on many factors that, taken together, can lead to seemingly inconsistent levels of enhancement... - Analysis of data fusion methods in virtual screening: similarity and group fusionMartin Whittle
Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, UK
J Chem Inf Model 46:2206-19. 2006..The methods are extended to analyze the comparatively successful results of group fusion with multiple actives, and we provide a rationale for the observed superiority of the MAX-rule over the SUM-rule in this context... - Sequence-dependent DNA structure: a database of octamer structural parametersEleanor J Gardiner
Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
J Mol Biol 332:1025-35. 2003..The TA step stands out as the most flexible sequence element with respect to decreasing twist and increasing roll. However, as with the structural properties, this behavior is highly context-dependent and some TA steps are very straight... - GAPDOCK: a Genetic Algorithm Approach to Protein Docking in CAPRI round 1Eleanor J Gardiner
Department of Information Studies, Krebs Institute, Sheffield University, Sheffield, United Kingdom
Proteins 52:10-4. 2003..Nevertheless, it is clear that there is a need for improved methods for distinguishing between "correct" and "plausible but incorrect" complexes... - Designing focused libraries using MoSELECTValerie J Gillet
Department of Information Studies, Krebs Institute for Biomolecular Research, University of Sheffield, Western Bank, UK
J Mol Graph Model 20:491-8. 2002..Experiments are reported where MoSELECT has been applied to the design of various focused libraries... - Analysis and use of fragment-occurrence data in similarity-based virtual screeningShereena M Arif
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield, S1 4DP, UK
J Comput Aided Mol Des 23:655-68. 2009.... - Evaluation of similarity measures for searching the dictionary of natural products databaseMartin Whittle
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
J Chem Inf Comput Sci 43:449-57. 2003.... - Calculating the knowledge-based similarity of functional groups using crystallographic dataP Watson
Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, UK
J Comput Aided Mol Des 15:835-57. 2001..Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs... - Virtual screening using binary kernel discrimination: analysis of pesticide dataDavid J Wilton
Department of Information Studies, University of Sheffield, Sheffield S10 2TN, UK
J Chem Inf Model 46:471-7. 2006..Similar conclusions resulted from application of the methods to a pesticide data set for which categorical activity data were available... - Assessment of additive/nonadditive effects in structure-activity relationships: implications for iterative drug designYogendra Patel
Department of Information Studies, University of Sheffield, Regent Court, 211 Portobello Street, Sheffield S14DP, United Kingdom
J Med Chem 51:7552-62. 2008..These attributes can provide guidelines on when it is appropriate to apply FW analysis as well as for library design, and they also have important implications for further steps in iterative drug design... - Evaluation of machine-learning methods for ligand-based virtual screeningBeining Chen
Department of Chemistry, University of Sheffield, Western Bank, Sheffield, UK
J Comput Aided Mol Des 21:53-62. 2007..In such cases, a simpler approach based on group fusion would appear to provide superior screening performance, especially when structurally heterogeneous datasets are to be processed... - Similarity searching in databases of flexible 3D structures using autocorrelation vectors derived from smoothed bounded distance matricesNicholas Rhodes
Department of Information Studies, The University of Sheffield, Regent Court, 211 Portobello Street, Sheffield, South Yorkshire, S1 4DP, United Kingdom
J Chem Inf Model 46:615-9. 2006.... - Protein docking using a genetic algorithmE J Gardiner
Department of Information Studies and Department of Molecular Biology and Biotechnology, Krebs Institute, Sheffield University, Sheffield, United Kingdom
Proteins 44:44-56. 2001..We have also successfully reassembled a 1,400-residue heptamer based on the top-ranking GA solution obtained when docking two bound subunits... - The EVA spectral descriptorD B Turner
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, S10 2TN, Sheffield, UK
Eur J Med Chem 35:367-75. 2000..Brief comment is made on the use of the EVA descriptor for diversity studies and the similarity searching of chemical structure databases... - Structural DNA profiles: single sequence queriesLinda Hirons
Centre for Chemical Biology, Krebs Institute for Biomolecular Science, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
J Chem Inf Model 46:743-52. 2006..Two sequences that are similar by their nucleotide composition but are known to be very different by structure are analyzed, resulting in useful illustrations that agree with the experimental nuclear magnetic resonance structures... - Use of reduced graphs to encode bioisosterism for similarity-based virtual screeningKristian Birchall
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Sheffield S1 4DP, United Kingdom
J Chem Inf Model 49:1330-46. 2009..This presents serious problems for the routine use of information about bioisosteric fragments in similarity-based virtual screening... - Protein structures and information extraction from biological texts: the PASTA systemR Gaizauskas
Department of Computer Science, University of Sheffield, Western Bank, UK
Bioinformatics 19:135-43. 2003..dcs.shef.ac.uk/nlp/pasta/. The evaluation resources (manually annotated corpora) are also available through the website: http://www.dcs.shef.ac.uk/nlp/pasta/results.html... - Effect of data standardization on chemical clustering and similarity searchingChia Wei Chu
Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, UK
J Chem Inf Model 49:155-61. 2009.... - Alignment of three-dimensional molecules using an image recognition algorithmNicola J Richmond
Department of Information Studies, Krebs Institute for Biomolecular Research, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
J Mol Graph Model 23:199-209. 2004..A range of examples is provided to demonstrate the efficiency and effectiveness of the method... - A fourier fingerprint-based method for protein surface representationMartin J Bayley
Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
J Chem Inf Model 45:696-707. 2005..Searching experiments using these fingerprints on a set of 366 proteins demonstrate that this provides an effective and an efficient technique for the matching of protein surfaces... - Identification of target-specific bioisosteric fragments from ligand-protein crystallographic dataElizabeth A Kennewell
Krebs Institute of Biomolecular Research and Department of Information Studies, University of Sheffield, Sheffield, S1 4DP, UK
J Comput Aided Mol Des 20:385-94. 2006..Experiments with 12 sets of ligand-protein complexes from the Protein Data Bank demonstrate the effectiveness of the procedure... - Representation, searching and discovery of patterns of bases in complex RNA structuresAnne-Marie Harrison
Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
J Comput Aided Mol Des 17:537-49. 2003..An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA... - Evaluation of molecular similarity and molecular diversity methods using biological activity dataPeter Willett
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, United Kingdom
Methods Mol Biol 275:51-64. 2004..The evaluation criteria considered are based on biological activity data, both qualitative and quantitative, with rather different criteria needing to be used depending on the type of data available... - Analysis of neighborhood behavior in lead optimization and array designGeorge Papadatos
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, 211 Portobello Street, Sheffield S1 4DP, United Kingdom
J Chem Inf Model 49:195-208. 2009..Evidence is provided to suggest that the optimality criterion method may provide a better quantitative description of neighborhood behavior than the optimal diagonal method... - Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databasesJohn W Raymond
Pfizer Global Research and Development, Ann Arbor Laboratories, Michigan 48105, USA
J Comput Aided Mol Des 16:59-71. 2002..Our results suggest that graph-based approaches provide an effective complement to existing fingerprint-based approaches to virtual screening... - Comparison of chemical clustering methods using graph- and fingerprint-based similarity measuresJohn W Raymond
Pfizer Global Research and Development, Ann Arbor Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, USA
J Mol Graph Model 21:421-33. 2003.... - Fast diagnosis with sensors of uncertain qualityOzgur Erdinc
IEEE Trans Syst Man Cybern B Cybern 38:1157-65. 2008..We provide results illustrating performance in terms of both computational needs and error rate, and show its application both as a filter (i.e., used to "clean" sensor reports) and as a standalone state estimator... - Unsupervised 3D ring template searching as an ideas generator for scaffold hopping: use of the LAMDA, RigFit, and field-based similarity search (FBSS) methodsMartin Bohl
TRIPOS GmbH, Martin Kollar Strasse 17, D 81829 Munich, Germany
J Chem Inf Model 46:1882-90. 2006..Not only are the methods effective but some are sufficiently rapid to permit scaffold searching in large chemical databases on a routine basis... - A sphere-based descriptor for matching protein structuresShin ichi Nakayama
University of Library and Information Science, 1 2 Kasuga, Tsukuba, Ibaraki 305 8550, Japan
J Mol Model 8:199-207. 2002..The results indicate that the method can quickly align protein sequences considering the 3D structure and can find proteins that are 3D structurally similar and dissimilar to the target protein... - Structure and singly occupied molecular orbital analysis of anionic tautomers of guanineMaciej Haranczyk
Department of Chemistry, University of Gdansk, 80 952 Gdansk, Poland
J Comput Chem 29:1277-91. 2008..They also form an "island of stability" in the tautomeric space of guanine... - Maximum common subgraph isomorphism algorithms for the matching of chemical structuresJohn W Raymond
Pfizer Global Research and Development, Ann Arbor Laboratories, 2800 Plymouth Road, Ann Arbor, Michigan 48105, USA
J Comput Aided Mol Des 16:521-33. 2002.... - Frequency tracking in optical Doppler tomography using an adaptive notch filterYueli Chen
University of Connecticut, Electrical and Computer Engineering Department, Storrs, Connecticut 06269, USA
J Biomed Opt 12:014018. 2007..Our simulations and imaging results also demonstrate that this filter has good performance in terms of noise robustness and estimation accuracy compared with existing estimation algorithms...