Chemoinformatics at the University of Sheffield 2002–2014

This paper summarises work in chemoinformatics carried out in the Information School of the University of Sheffield during the period 2002–2014. Research studies are described on fingerprint‐based similarity searching, data fusion, applications of reduced graphs and pharmacophore mapping, and on the School’s teaching in chemoinformatics.

[1]  P. Willett.  Searching techniques for databases of two- and three-dimensional chemical structures. , 2005, Journal of medicinal chemistry.

[2]  Peter Willett,et al.  Inverse Frequency Weighting of Fragments for Similarity-Based Virtual Screening , 2010, J. Chem. Inf. Model..

[3]  Jérôme Hert,et al.  Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures , 2004, J. Chem. Inf. Model..

[4]  Valerie J. Gillet,et al.  Development and validation of an improved algorithm for overlaying flexible molecules , 2012, Journal of Computer-Aided Molecular Design.

[5]  Peter Willett,et al.  Representation, searching and discovery of patterns of bases in complex RNA structures , 2003, J. Comput. Aided Mol. Des..

[6]  John B. O. Mitchell.  Machine learning methods in chemoinformatics , 2014, Wiley interdisciplinary reviews. Computational molecular science.

[7]  Peter Willett,et al.  Similarity methods in chemoinformatics , 2009, Annu. Rev. Inf. Sci. Technol..

[8]  Ronan Bureau,et al.  Clustering files of chemical structures using the Székely-Rizzo generalization of Ward's method. , 2009, Journal of molecular graphics & modelling.

[9]  P. Willett,et al.  Combining multiple classifications of chemical structures using consensus clustering. , 2012, Bioorganic & medicinal chemistry.

[10]  Peter Willett,et al.  Effectiveness of 2D fingerprints for scaffold hopping. , 2011, Future medicinal chemistry.

[11]  Peter Willett,et al.  RASCAL: Calculation of Graph Similarity using Maximum Common Edge Subgraphs , 2002, Comput. J..

[12]  Peter Willett,et al.  Enhancing the Effectiveness of Virtual Screening by Fusing Nearest Neighbor Lists: A Comparison of Similarity Coefficients , 2004, J. Chem. Inf. Model..

[13]  Peter Willett,et al.  Representing Clusters Using a Maximum Common Edge Substructure Algorithm Applied to Reduced Graphs and Molecular Graphs , 2007, J. Chem. Inf. Model..

[14]  Peter Willett,et al.  Chemoinformatics Research at the University of Sheffield: A History and Citation Analysis , 2003, J. Inf. Sci..

[15]  Valerie J. Gillet,et al.  Computer storage and retrieval of generic chemical structures in patents. 8. Reduced chemical graphs and their applications in generic chemical structure retrieval , 1987, J. Chem. Inf. Comput. Sci..

[16]  Peter Willett,et al.  Graph theoretic methods for the analysis of structural relationships in biological macromolecules , 2005, J. Assoc. Inf. Sci. Technol..

[17]  Michael F. Lynch,et al.  Information retrieval research in the Department of Information Studies, University of Sheffield: 1965-1985 , 1987, J. Inf. Sci..

[18]  Gavin Harper,et al.  Evolving Interpretable Structure-Activity Relationships. 1. Reduced Graph Queries , 2008, J. Chem. Inf. Model..

[19]  Ian A. Watson,et al.  ErG: 2D Pharmacophore Descriptions for Scaffold Hopping , 2006, J. Chem. Inf. Model..

[20]  Valerie J. Gillet,et al.  Emerging Pattern Mining To Aid Toxicological Knowledge Discovery , 2014, J. Chem. Inf. Model..

[21]  Robert P. Sheridan,et al.  Chemical Similarity Using Physiochemical Property Descriptors , 1996, J. Chem. Inf. Comput. Sci..

[22]  Peter Willett,et al.  Implementation of nearest-neighbor searching in an online chemical structure search system , 1986, J. Chem. Inf. Comput. Sci..

[23]  Valerie J. Gillet,et al.  Knowledge-Based Approach to de Novo Design Using Reaction Vectors , 2009, J. Chem. Inf. Model..

[24]  Matthias Rarey,et al.  Feature trees: A new molecular similarity measure based on tree matching , 1998, J. Comput. Aided Mol. Des..

[25]  G. Harper,et al.  The reduced graph descriptor in virtual screening and data-driven clustering of high-throughput screening data. , 2004, Journal of chemical information and computer sciences.

[26]  Peter Willett,et al.  Similarity-based virtual screening using 2D fingerprints. , 2006, Drug discovery today.

[27]  Peter Willett,et al.  Combination of Similarity Rankings Using Data Fusion , 2013, J. Chem. Inf. Model..

[28]  Valerie J. Gillet,et al.  Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques , 2004, J. Comput. Aided Mol. Des..

[29]  Valerie J. Gillet,et al.  Multiobjective Optimization of Pharmacophore Hypotheses: Bias Toward Low-Energy Conformations , 2009, J. Chem. Inf. Model..

[30]  Peter Willett,et al.  Combination Rules for Group Fusion in Similarity‐Based Virtual Screening , 2010, Molecular informatics.

[31]  Peter Willett,et al.  Scaffold Hopping Using Clique Detection Applied to Reduced Graphs , 2006, J. Chem. Inf. Model..

[32]  Peter Willett,et al.  Analysis of Data Fusion Methods in Virtual Screening: Similarity and Group Fusion , 2006, J. Chem. Inf. Model..

[33]  Peter Ertl,et al.  Bioisosteric Replacement and Scaffold Hopping in Lead Generation and Optimization , 2010, Molecular informatics.

[34]  Valerie J Gillet,et al.  Designing combinatorial libraries optimized on multiple objectives. , 2004, Methods in molecular biology.

[35]  Peter Willett,et al.  Use of Reduced Graphs To Encode Bioisosterism for Similarity-Based Virtual Screening , 2009, J. Chem. Inf. Model..

[36]  P. Willett,et al.  PHARMACOPHORE PERCEPTION , DEVELOPMENT , AND USE IN DRUG DESIGN , 2011 .

[37]  Valerie J. Gillet,et al.  Incorporating partial matches within multiobjective pharmacophore identification , 2006, J. Comput. Aided Mol. Des..

[38]  Peter Willett,et al.  Evaluation of a Bayesian inference network for ligand-based virtual screening , 2009, J. Cheminformatics.

[39]  Maik Moeller,et al.  An Introduction To Chemoinformatics , 2016 .

[40]  István Ujváry,et al.  Extended Summary: BIOSTER—a database of structurally analogous compounds , 1997 .

[41]  Gavin Harper,et al.  Evolving Interpretable Structure-Activity Relationship Models. 2. Using Multiobjective Optimization To Derive Multiple Models , 2008, J. Chem. Inf. Model..

[42]  M. F. Lynch,et al.  Chemical structure retrieval : a review of current research in the Department of Information Studies, University of Sheffield , 1990 .

[43]  Peter Willett,et al.  A bibliometric analysis of the literature of chemoinformatics , 2008, Aslib Proc..

[44]  Peter Willett,et al.  A bibliometric analysis of the Journal of Molecular Graphics and Modelling. , 2007, Journal of molecular graphics & modelling.

[45]  Peter Willett,et al.  GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D , 2006, J. Comput. Aided Mol. Des..

[46]  Mohd Firdaus Raih,et al.  COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures , 2014, Nucleic Acids Res..

[47]  W. Patrick Walters,et al.  Chapter 8 Machine Learning in Computational Chemistry , 2006 .

[48]  R. Venkataraghavan,et al.  Atom pairs as molecular features in structure-activity studies: definition and applications , 1985, J. Chem. Inf. Comput. Sci..

[49]  Valerie J. Gillet,et al.  Analysis of Data Fusion Methods in Virtual Screening: Theoretical Model , 2006, J. Chem. Inf. Model..

[50]  P. Willett,et al.  Enhancing the effectiveness of similarity-based virtual screening using nearest-neighbor information. , 2005, Journal of medicinal chemistry.

[51]  Mohd Firdaus Raih,et al.  SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures , 2012, Nucleic Acids Res..

[52]  Rachelle J. Bienstock,et al.  Library design, search methods, and applications of fragment-based drug design , 2011 .

[53]  Belur V. Dasarathy.  A representative bibliography of surveys in the information fusion domain , 2010, Inf. Fusion.

[54]  Peter Willett,et al.  Algorithms for the identification of three-dimensional maximal common substructures , 1987, J. Chem. Inf. Comput. Sci..

[55]  Jérôme Hert,et al.  New Methods for Ligand-Based Virtual Screening: Use of Data Fusion and Machine Learning to Enhance the Effectiveness of Similarity Searching , 2006, J. Chem. Inf. Model..

[56]  Jonathan D Hirst,et al.  Machine learning in virtual screening. , 2009, Combinatorial chemistry & high throughput screening.

[57]  Visakan Kadirkamanathan,et al.  Lead Optimization Using Matched Molecular Pairs: Inclusion of Contextual Information for Enhanced Prediction of hERG Inhibition, Solubility, and Lipophilicity , 2010, J. Chem. Inf. Model..

[58]  Paolo Massimo Buscema,et al.  Similarity Coefficients for Binary Chemoinformatics Data: Overview and Extended Comparison Using Simulated and Real Data Sets , 2012, J. Chem. Inf. Model..

[59]  Jeff Morris,et al.  Further Development of Reduced Graphs for Identifying Bioactive Compounds , 2003, J. Chem. Inf. Comput. Sci..

[60]  David J Wild,et al.  Challenges for chemoinformatics education in drug discovery. , 2006, Drug discovery today.

[61]  Valerie J. Gillet,et al.  Automating Knowledge Discovery for Toxicity Prediction Using Jumping Emerging Pattern Mining , 2012, J. Chem. Inf. Model..

[62]  Jérôme Hert,et al.  Turbo similarity searching: Effect of fingerprint and dataset on virtual‐screening performance , 2009, Stat. Anal. Data Min..

[63]  Yvonne C. Martin,et al.  A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists , 1993, J. Comput. Aided Mol. Des..

[64]  Peter Willett,et al.  The Journal of Chemical Documentation and the Journal of Chemical Information and Computer Sciences: Publication and Citation Statistics , 2010, J. Chem. Inf. Model..

[65]  Valerie J. Gillet,et al.  Compression of Molecular Interaction Fields Using Wavelet Thumbnails: Application to Molecular Alignment , 2012, J. Chem. Inf. Model..

[66]  John Bradshaw,et al.  Similarity Searching Using Reduced Graphs , 2003, J. Chem. Inf. Comput. Sci..

[67]  P. Willett,et al.  A Comparison of Some Measures for the Determination of Inter‐Molecular Structural Similarity Measures of Inter‐Molecular Structural Similarity , 1986 .

[68]  Gareth Jones,et al.  A genetic algorithm for flexible molecular overlay and pharmacophore elucidation , 1995, J. Comput. Aided Mol. Des..

[69]  Yoshimasa Takahashi,et al.  Automatic identification of molecular similarity using reduced-graph representation of chemical structure , 1992, J. Chem. Inf. Comput. Sci..

[70]  G. Maggiora,et al.  Molecular similarity in medicinal chemistry. , 2014, Journal of medicinal chemistry.

[71]  Peter Willett,et al.  Searching for Patterns of Amino Acids in 3D Protein Structures , 2003, J. Chem. Inf. Comput. Sci..

[72]  Andrew R. Leach,et al.  A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP , 2002, J. Comput. Aided Mol. Des..

[73]  Gavin Harper,et al.  Training Similarity Measures for Specific Activities: Application to Reduced Graphs , 2006, J. Chem. Inf. Model..

[74]  E. A. Fox,et al.  Combining the Evidence of Multiple Query Representations for Information Retrieval , 1995, Inf. Process. Manag..

[75]  Peter Willett,et al.  Similarity Searching in Files of Three-Dimensional Chemical Structures: Evaluation of the EVA Descriptor and Combination of Rankings Using Data Fusion , 1997, J. Chem. Inf. Comput. Sci..

[76]  Charles L. A. Clarke,et al.  Reciprocal rank fusion outperforms condorcet and individual rank learning methods , 2009, SIGIR.

[77]  Peter Willett,et al.  From chemical documentation to chemoinformatics: 50 years of chemical information science , 2008, J. Inf. Sci..

[78]  Peter Willett,et al.  Promoting Access to White Rose Research Papers Enhancing the Effectiveness of Ligand-based Virtual Screening Using Data Fusion , 2022 .

[79]  Richard A. Lewis,et al.  Three-dimensional pharmacophore methods in drug discovery. , 2010, Journal of medicinal chemistry.

[80]  Peter Willett,et al.  Alignment of three-dimensional molecules using an image recognition algorithm. , 2004, Journal of molecular graphics & modelling.

[81]  Peter Willett,et al.  Analysis and use of fragment-occurrence data in similarity-based virtual screening , 2009, J. Comput. Aided Mol. Des..