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This page lists numerous publications authored or co-authored by Digital Chemistry's Directors, along with references to relevant papers by our clients. We hope these may be useful if you are interested in our research or are looking for greater scientific detail than can be included elsewhere on this website.

Recent Publications include:

  • BIOSTER: A Database of Bioisosteres and Bioanalogues; István Ujváry and Julian Hayward, Methods and Principles in Medicinal Chemistry (Volume 54): Bioisosteres in Medicinal Chemistry (Ed. Nathan Brown) (Wiley-VCH, 2012) [ISBN 978-3-527-33015-7].
  • Theilheimer's Synthetic Methods of Organic Synthesis (Volumes 72-84) (Ed. Gill Tozer-Hotchkiss) (Karger, 2007-2014)
  • Chemical patent information systems; Geoffrey M. Downs and John M. Barnard, Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011, 1 (5), 727-41 [DOI: 10.1002/wcms.41].
  • Computer-aided synthesis design: 40 years on; Anthony Cook, A. Peter Johnson, James Law, Mahdi Mirzazadeh, Orr Ravitz and Aniko Simon, Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011 (on-line) [DOI: 10.1002/wcms.61].
  • Representing Chemical Structures in Databases for Drug Design; John M. Barnard, Peter W. Kenny and Paul N. Wallace in "Drug Design Strategies: Quantitative Approaches" eds. D. Livingstone and A. Davis (RSC Publishing, 2012) [ISBN: 978-1-84973-341-0].

Older publications are archived into themed categories and annotated with further detail for your convenience.
Some papers appear in more than one category.


 
Chemical Fragment Descriptors and Fingerprints

Chemical structures can be described by "fingerprints", which are strings of ones and zeros, representing the presence or absence of particular structural fragments in the molecule. These fingerprints can be very useful for clustering and diversity analysis and for identifying structural features significant for example for biological activity. The choice of fragments to use is obviously important and Digital Chemistry's fingerprint-generation software can create and use customised dictionaries of fragments, offering greater flexibility to the user. Digital Chemistry's fingerprints have performed well in a number of comparative studies.

  • Downs, G.M.; Gill, G.S.; Willett, P.; Walsh, P. (1995) Automated descriptor selection and hyper structure generation to assist SAR studies, SAR and QSAR Env. Res., 3 (4), 253-264.
The reference below gives a brief summary of our products, which was presented as a "Product Review" at the 1996 International Conference on Chemical Structures, Noordwijkerhout, The Netherlands.
  • Barnard, J.M.; Downs, G.M. (1997a) Chemical Fragment Generation and Clustering Software, J. Chem. Inf. Comput. Sci., 37 (1), 141-142.
This paper gives an independent comparison of commercial software, including ours.
  • Warr, W. A. (1997) Commercial software systems for diversity analysis. In Computational Methods for the Analysis of Molecular Diversity, Willett, P. (Ed.) Perspectives in Drug Discovery and Design, 7/8, 115-130.
The following papers discuss the use of BCI fingerprints for diversity analysis.
  • Van Geerestein, V. J.; Hamersma, H.; van Helden, S. P. (1997) Exploiting molecular diversity: pharmacophore searching and compound clustering. In Computer Assisted Lead Finding and Optimization, van de Waterbeemd, H.; Testa, B.; Folkers, G. (Eds.), Wiley-VCH, Basel, pp. 159-178
  • Bayada, D. M.; Hamersma, H.; van Geerestein, V. J. (1999) Molecular diversity and representativity in chemical databases. J. Chem. Inf. Comput. Sci., 39, 1-10.
  • Wild, D.; Blankley, C. J. (2000) Comparison of 2D Fingerprint types and hierarchy level selection methods for structural grouping using Ward's clustering. J. Chem. Inf. Comput. Sci., 40, 155-162.
  • Wagener, M.; van Geerestein, V. J. (2000) Potential drugs and nondrugs: prediction and identification of important structural features. J. Chem. Inf. Comput. Sci., 40, 280-292.
 
Chemical Structure Similarity and Clustering
Structure fingerprints are very useful for obtaining a quantitative measure of the similarity between two molecules. Similarity or distance measures form the basis of cluster analysis, which allows large datasets of chemical structures to be grouped into classes, often hierarchically related. Digital Chemistry has developed software specifically for the cluster analysis of very large chemical datasets, which is widely used in the industry, and John Barnard and Geoff Downs have contributed a number of review articles on the subject.
  • Rasmussen, E.M.; Downs, G.M.; Willett, P. (1988) Automatic classification of chemical structure databases using a highly parallel array processor, J. Comp. Chem., 9 (4), 378-386.
  • Downs, G.M.; Walsh, P.T.; Booth, A.M. (1990) Similarity and clustering of chemical structures for property prediction. Presented at the 2nd International Workshop on Computer Chemistry: Structure-property relations, at the Technical University, Merseburg, Germany, 2-4 October 1990. (HSE Report IR/L/FT/90/6)
  • Downs, G.M.; Willett, P. (1991) The use of similarity and clustering techniques for the prediction of molecular properties, In Applied Multivariate Analysis in SAR and Environmental Studies, Devillers, J.; Karcher, W. (Eds.). Kluwer Academic Publishers, Dordrecht, pp. 247-280.
This general review of the subject has been frequently cited in the literature.
  • Barnard, J.M.; Downs, G.M. (1992) Clustering of chemical structures on the basis of two-dimensional similarity measures, J. Chem. Inf. Comput. Sci., 32, 644-649.
  • Downs, G.M.; Poirette, A.R.; Walsh, P.T.; Willett, P. (1993) Evaluation of similarity searching methods using activity and toxicity data, In: Chemical Structures 2, Warr, W.A. (Ed.), Springer-Verlag, Berlin, pp. 409-421.
The study documented below, carried out jointly with Chemical Abstracts Service and Sheffield University, was the first to demonstrate the superiority of hierarchical clustering methods, such as Ward's, over the more commonly-used Jarvis-Patrick non-hierarchical method.
  • Downs, G.M.; Willett, P.; Fisanick, W. (1994) Similarity searching and clustering of chemical-structure databases using molecular property data, J. Chem. Inf. Comput. Sci., 34 (5), 1094-1102.
  • Downs, G.M.; Willett, P. (1994) Clustering of chemical structure databases for compound selection. In Advanced Computer-Assisted Techniques in Drug Discovery, van de Waterbeemd, H. (Ed.) VCH, Weinheim, 1994, pp. 111-130.
  • Downs, G.M. Willett, P. (1995) Similarity searching in databases of chemical structures, Reviews in Computational Chemistry, 7, 1-66.
A brief summary of our products, which was presented as a "Product Review" at the 1996 International Conference on Chemical Structures, Noordwijkerhout, The Netherlands.
  • Barnard, J.M.; Downs, G.M. (1997a) Chemical Fragment Generation and Clustering Software, J. Chem. Inf. Comput. Sci., 37 (1), 141-142
The reference below describes an important study, from Abbott Laboratories, which confirmed the superiority of Ward's algorithm for clustering chemical structures. Several of our clustering algorithm implementations were used in the comparison.
  • Brown, R.D.; Martin, Y.C. (1996) Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection, J. Chem. Inf. Comput. Sci., 36 (3), 572-584
This is a follow-up study from Abbott, to that above, which also made use of our software.
  • Brown, R.D.; Martin, Y.C. (1997) The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding, J. Chem. Inf. Comput. Sci., 37 (1) 1-9
An independent comparison of commercial software, including BCI's.
  • Warr, W. A. (1997) Commercial software systems for diversity analysis. In Computational Methods for the Analysis of Molecular Diversity, Willett, P. (Ed.) Perspectives in Drug Discovery and Design, 7/8, 115-130
The following four papers are recent review articles, covering descriptors, similarity measures, clustering techniques and applications.
  • Willett, P.; Barnard, J. M.; Downs, G. M. (1998) Chemical Similarity Searching. J. Chem. Inf. Comput. Sci., 38 (6) 983-996
  • Barnard, J. M.; Downs, G. M.; Willett, P. (2000) Descriptor-Based Similarity Measures for Screening Chemical Databases. In Virtual Screening for Bioactive Molecules, Böhm, H.-J. et al. (Eds.). Wiley, pp. 59-80
  • Downs, G.M.; Barnard, J.M. (2002) Clustering methods and their uses in computational chemistry. Reviews in Computational Chemistry, 18, 1-40.
  • Downs, G. M. (2004) Molecular Descriptors. In Computational Medicinal Chemistry for Drug Discovery, Bultinck, P.; De Winter, H.; Langenaeker, W.; Tollenaere, J. P. (Eds.). New York: Marcel Dekker, pp 515-538.
 
Markush Structures and Combinatorial Libraries

"Markush" or Generic structures are structures with R-groups, representing classes of molecules with common structural features. They are best known for their occurrence in the chemical patent literature but in recent years they have also been found useful for description of combinatorial libraries, where BCI (and now Digital Chemistry) has pioneered their use for rapid generation of structure descriptors.

This paper is a preliminary report on the use of Markush structure-handling techniques for rapid generation of fragment-based fingerprints for combinatorial libraries.

  • Downs, G.M.; Barnard, J.M. (1997) Techniques for Generating Descriptive Fingerprints in Combinatorial Libraries. J. Chem. Inf. Comput. Sci., 37 (1), 59-61
This is a review of the available methods for computer handling of combinatorial libraries, particularly discussing their usefulness for different purposes, and interconversion.
  • Barnard, J.M.; Downs, G.M. (1997b) Computer Representation and Manipulation of Combinatorial Libraries. In Computational methods for the Analysis of Molecular Diversity, Willett, P. (Ed.) Perspectives in Drug Discovery and Design, 7/8, 13-30
  • Barnard, J. M.; Downs, G. M.; von Scholley-Pfab, A.; Brown, R.D. (2000) Use of Markush structure analysis techniques for descriptor generation and clustering of large combinatorial libraries. J. Mol. Graph. Modelling, 18 (4/5) 452-463
 
Chemical Structure Representation
Many different formats are used for the representation of chemical structures in computer systems. Several of the papers in this section are concerned with attempts to develop a standard interchange format for chemical structures, with which BCI was involved during the late 1980s and early 1990s. The SMD format (*Barnard, 1990) has never achieved any significant use, though many of its ideas were incorporated in the MIF format (**Allen et al., 1995), which has enjoyed some used in the crystallographic community. Concepts worked on by Tony Cook at this time also influenced the development of the STAR dictionary language (***Hall and Cook, 1995). The issue of standard formats is discussed in ****Barnard (1998).
  • Barnard, J.M. (1988a) Towards a standard interchange format for chemical structure data, Proceedings of the 12th International Online Information Meeting, pp. 605-609. Oxford: Learned Information.
  • Barnard, J.M. (1989a) Standard representations for chemical information, Proceedings of the Montreux 1989 International Chemical Information Conference, Calne: Infonortics Ltd.
This paper concerns the original publication concerning the ROSDAL line notation, which was developed on contract for the Beilstein Institute, and is widely used in Beilstein's products.
  • Barnard, J.M.; Jochum, C.J; Welford, S.M. (1989) ROSDAL: A universal structure/substructure representation for PC-host communication. In Chemical Structure Information Systems, Warr, W.A. (Ed.) ACS Symposium Series, 400, pp. 76-81. Washington: American Chemical Society.
  • *Barnard, J.M. (1990) Draft specification for revised version of the Standard Molecular Data (SMD) Format, J. Chem. Inf. Comput. Sci., 30, 81-96.
This is a review of methods for representing stereochemistry in connection tables.
  • Barnard, J.M.; Cook, A.P.F.; Rohde, B. (1990) Storing and searching of stereochemistry in substructure search systems, In Chemical Information Systems Beyond the Structure Diagram, Bawden, D.; Mitchell, E. (Eds.). Chichester Ellis Horwood.
This general review is a chapter for a textbook.
  • Barnard, J.M. (1991a) Structure representation and searching, In Chemical Structure Systems, Ash, J.E.; Warr, W.A.; Willett, P. (Eds.) Chichester: Ellis Horwood.
  • **Allen, F.H.; Barnard, J.M.; Cook, A.P.F.; Hall, S.R. (1995) The Molecular Information File. Core Specifications of a new Standard Format for Chemical Information, J. Chem. Inf. Comput. Sci., 35, 412-427
This is an update of the review in Barnard (1991a).
  • ****Barnard, J.M. (1998) Structure Representation and Search, In Encyclopedia of Computational Chemistry, Schleyer, P. von R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F.; Shreiner, P. R. (Eds.). Wiley, Chichester, 4, 2818-2826
  • Barnard, J. M. (2003) Representation of chemical structures - overview. In Handbook of Chemoinformatics, Gasteiger, J. (Ed.). Wiley-VCH, 1, 27-50.
  • ***Hall, S. R.; Cook, A. P. F. (1995) STAR dictionary language: initial specification, J. Chem. Inf. Comput. Sci., 35, 819-825
  • Hopkinson, G. A.; Cook, A. P. F.; Buchan, I.P. (1990) Computer treatment of chemical reactions and synthesis problems. In Chemical Information Systems Beyond the Structure Diagram, Bawden, D.; Mitchell, E. (Eds.) pp. 83-91. Chichester: Ellis Horwood.
  • Johnson, A. P.; Burt, K.; Cook, A. P. F.; Higgins, K. M.; Hopkinson, G.A.; Singh, G. (1989) Integration and standards: use of a host language interface. In Chemical Structure Information Systems, Warr, W.A. (Ed.). ACS Symposium Series, 400, pp. 50-58. Washington: American Chemical Society.
 
Chemical Structure Searching
The searching of large databases of chemical structures to find those containing a particular substructure requires the use of specialised and efficient algorithms.
  • Downs, G.M.; Lynch, M.F.; Willett, P.; Manson, G.A.; Wilson, G.A. (1988) Transputer implementations of chemical substructure searching algorithms, Tetrahedron Computer Methodology, 1 (3), 207-217
This reference is for a general review of available algorithms, which was later updated and expanded as Barnard (1993)
  • Barnard, J.M. (1988b) Problems of substructure search and their solution, In Chemical Structures: the International Language of Chemistry; Proceedings of a conference held at the Leeuwenhorst Congress Center, Noordwijkerhout, The Netherlands, 31 May to 4 June 1987. Warr, W.A. (Ed.) pp. 113-126.
    Heidelberg: Springer Verlag.
This general review is a chapter for a textbook.
  • Barnard, J.M. (1991a) Structure representation and searching, In Chemical Structure Systems, Ash, J.E.; Warr, W.A.; Willett, P. (Eds.) Chichester: Ellis Horwood.
  • Brown, R.D.; Downs, G.M.; Willett, P. (1992) A hyperstructure model for chemical structure handling: generation and atom-by-atom searching of hyperstructures, J. Chem. Inf. Comput. Sci., 32 (5), 522-531
As referred to above, this is a general review of the available algorithms, updating and expanding on Barnard (1988b).
  • Barnard, J.M. (1993) Substructure searching methods: old and new, J. Chem. Inf. Comput. Sci., 33, 532-538.
  • Brown, R.D.; Downs, G.M.; Jones, G.; Willett, P. (1994) Hyperstructure model for chemical structure handling: techniques for substructure searching. J. Chem. Inf. Comput. Sci., 34 (1), 47-53
The first part of this paper is a review of the available algorithms, based largely on the material of Barnard (1993); the second part provides a description of the algorithm used in Beilstein's CrossFire software.
  • Barnard, J.M.; Walkowiak, D. (1997) Computer Systems for Substructure Searching. Chapter 5 in The Beilstein System: Strategies for Effective Searching, Heller, S. R. (Ed.). Washington: American Chemical Society
An update of the review in Barnard (1991a) above.
  • Barnard, J.M. (1998) Structure Representation and Search. In Encyclopedia of Computational Chemistry, Schleyer, P. von R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F.; Shreiner, P. R. (Eds.). Wiley, Chichester, 4, 2818-2826.
 
Markush Structures in Patents
Digital Chemistry Directors John Barnard and Geoff Downs both did postgraduate research into computer systems for storage and retrieval of Markush structures from patents. The first fifteen papers in this section are research publications from the Sheffield University project on this topic, to which they contributed as authors.
  • Lynch, M.F.; Barnard, J.M.; Welford, S.M. (1981) Computer storage and retrieval of generic structures in chemical patents. Part 1. Introduction and general strategy, J. Chem. Inf. Comput. Sci., 21 (3), 148-150
  • Barnard, J.M.; Lynch, M.F.; Welford, S.M. (1981) Computer storage and retrieval of generic structures in chemical patents. Part 2. GENSAL, a formal language for the description of generic chemical structures, J. Chem. Inf. Comput. Sci., 21 (3), 151-161
  • Welford, S.M.; Lynch, M.F.; Barnard, J.M. (1981) Computer storage and retrieval of generic structures in chemical patents. Part 3. Chemical grammars and their role in the manipulation of chemical structures, J. Chem. Inf. Comput. Sci., 21 (3), 161-168
  • Barnard, J.M.; Lynch, M.F.; Welford, S.M. (1982a) Computer storage and retrieval of generic structures in chemical patents. Part 4. An extended connection table representation for generic structures, J. Chem. Inf. Comput. Sci., 22 (3), 160-164
  • Welford, S.M.; Lynch, M.F.; Barnard, J.M. (1984) Computer storage and retrieval of generic structures in chemical patents. Part 5. Algorithmic generation of fragment descriptors for generic structure screening, J. Chem. Inf. Comput. Sci., 24 (2), 57-66
  • Barnard, J.M.; Lynch, M.F.; Welford, S.M. (1984) Computer storage and retrieval of generic structures in chemical patents. Part 6. An interpreter program for the generic structure description language GENSAL, J. Chem. Inf. Comput. Sci., 24 (2), 66-71
  • Gillet, V.J.; Welford, S.M.; Lynch, M.F., Willett, P.; Barnard, J.M.; Downs, G.M; Manson, G.; Thompson, J. (1986) Computer storage and retrieval of generic chemical structures in patents. 7. Parallel simulation of a relaxation algorithm for chemical substructure search, J. Chem. Inf. Comput. Sci., 26 (3), 118-126
  • Gillet, V.J.; Downs, G.M.; Ling, A.; Lynch, M.F.; Venkataram, P.; Wood, J.V.; Dethlefsen, W. (1987) Computer storage and retrieval of generic chemical structures in patents. Part 8 : Reduced chemical graphs and their applications in generic chemical structure retrieval, J. Chem. Inf. Comput. Sci., 27 (3), 126-137
  • Downs, G.M.; Gillet, V.J.; Holliday, J.D.; Lynch, M.F. (1989c) Computer storage and retrieval of generic chemical structures in patents. 9. An algorithm to find the extended set of smallest rings (ESSR) in structurally-explicit generics, J. Chem. Inf. Comput. Sci., 29 (3), 207-214
  • Downs, G.M.; Gillet, V.J.; Holliday, J.D.; Lynch, M.F. (1989d) Computer storage and retrieval of generic chemical structures in patents. 10. The generation and logical bubble-up of ring screens for structurally-explicit generics, J. Chem. Inf. Comput. Sci., 29 (3), 215-224
  • Dethlefsen, W.; Lynch, M.F., Gillet, V.J.; Downs, G.M.; Holliday, J.D.; Barnard, J.M. (1991a) Computer storage and retrieval of generic structures in patents. 11. Theoretical aspects of the use of structure languages in a retrieval system, J. Chem. Inf. Comput. Sci., 31 (2), 233-253
  • Dethlefsen, W.; Lynch, M.F.; Gillet, V.J.; Downs, G.M.; Holliday, J.D.; Barnard, J.M. (1991b) Computer storage and retrieval of generic structures in patents. 12. Principles of search operations involving parameter lists: matching relations, user-defined match levels and transition from the reduced graph search to the refined search, J. Chem. Inf. Comput. Sci., 31 (2), 253-260
  • Gillet, V.J.; Downs, G.M.; Holliday, J.D.; Lynch, M.F.; Dethlefsen, W.(1991) Computer storage and retrieval of generic chemical structures in patents. 13. Reduced graph generation, J. Chem. Inf. Comput. Sci., 31 (2), 253-260
  • Holliday, J.D.; Downs, G.M.; Gillet, V.J.; Lynch, M.F.; Dethlefsen, W.(1991) Computer storage and retrieval of generic chemical structures in patents. 14. Fragment generation from generic structures, J. Chem. Inf. Comput. Sci., 31 (2), 260-270
  • Holliday, J.D.; Downs, G.M.; Gillet, V.J.; Lynch, M.F.(1993) Computer storage and retrieval of generic chemical structures in patents. 15. Generation of topological fragment descriptors from non-topological representations of generic structure components, J. Chem. Inf. Comput. Sci., 33 (3), 369-377
The next group of papers in this section comprises review articles on storage and retrieval of Markush structures from patents. Most relate primarily to the Sheffield University project, though Barnard (1991b) and Berks, Barnard and O'Hara (1998) are more general in scope.
  • Barnard, J.M.; Lynch, M.F.; Welford, S.M. (1982b) Computer storage, retrieval and searching of generic chemical structures. Proceedings of the CNA(UK) Seminar on Structural Access to the Published Literature, Daresbury, March 1980. Chemical Notation Association (UK).
  • Welford, S.M.; Lynch, M.F.; Barnard, J.M. (1983) Towards simplified access to chemical structure information in the patent literature, J. Inf. Sci., 6, 3-10
  • Barnard, J.M. (1984a) (Ed.) Computer Handling of Generic Chemical Structures. Proceedings of a Conference organised by the Chemical Structure Association at the University of Sheffield, England, 26-29 March 1984. Aldershot: Gower.
  • Welford, S.M.; Ash, S.; Barnard, J.M.; Carruthers, L.; Lynch, M.F., von Scholley, A. (1984) The Sheffield University generic chemical structures research project, In Computer Handling of Generic Chemical Structures, Barnard, J. M. (Ed.) pp. 130-158. Aldershot: Gower, 1984.
  • Lynch, M.F.; Barnard, J.M.; Welford, S.M. (1985) Generic structure storage and retrieval, J. Chem. Inf. Comput. Sci., 25 (3), 264-270. [Invited contribution for the Silver Jubilee issue of the Journal.]
  • Barnard, J.M. (1987a) Online graphical searching of Markush structures in patents, Database, 10 (3) 27-34
  • Barnard, J.M. (1987b) New systems for chemical structures in patents. Proceedings of the 11th International Online Information Meeting, pp. 45-47. Oxford: Learned Information.
  • Lynch M.F.; Downs G.M.; Gillet V.J., Holliday J.D. (1989) Generic chemical structures in patents - an evaluation of the Sheffield University research work. In Proc. Montreux '89 International Chem. Info. Conf., 26-28 September 1989, pp 161-171
  • Barnard, J.M. (1991b) A comparison of different approaches to Markush structure handling, J. Chem. Inf. Comput. Sci., 31, 64-68
  • Berks, A.H.; Barnard, J.M.; O'Hara, P. (1998) Patent Databases and Markush Chemical Structure Search Systems. In Encyclopedia of Computational Chemistry, Schleyer, P. von R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F.; Shreiner, P. R. (Eds.). Wiley, Chichester, 3, 1552-1559
  • Downs, G. M.; Barnard, J. M. (1998) Chemical patents and structural information - the Sheffield research in context, J. Doc., 54, 106-120
This next paper describes a project in the early 1990s. The project is further discussed by Barnard (1991b).
  • Stiegler, G.; Maier, B.; Lenz, H. (1993) Automatic translation of GENSAL representation of Markush structures into GREMAS fragment codes at IDC, In Chemical Structures 2, Warr, W.A. (Ed.) Springer-Verlag, Berlin, pp. 105-114.
This recent paper describes ongoing work towards the in-house searching of chemical patents stored as Markush structures.
  • Barnard, J.; Wright, P.M. (2009) Towards In-House Searching of Markush Structures from Patents, World Patent Information, 31 (2), pp. 97-103. [DOI: 10.1016/j.wpi.2008.09.012]
 
Ring Perception in Chemical Structures

Identification of the rings present in a chemical structure is important for a number of different purposes, though it is not always obvious which of the various possible cyclical paths through a fused ring system are "useful". Geoff Downs' doctoral thesis involved the development of a new algorithm for identifying rings, and he has contributed a number of significant review articles to the literature.

This first paper is a comprehensive review of ring perception algorithms published up to 1989.
  • Downs, G.M.; Gillet, V.J.; Holliday, J.D.; Lynch, M.F. (1989a) Review of ring perception algorithms for chemical graphs, J. Chem. Inf. Comput. Sci., 29 (3), 172-187.
This describes the theoretical background to a novel ring-perception algorithm.
  • Downs, G.M.; Gillet, V.J.; Holliday, J.D.; Lynch, M.F. (1989b) Theoretical aspects of ring perception and development of the Extended Set of Smallest Rings concept, J. Chem. Inf. Comput. Sci., 29 (3), 187-206
A simplified review, discussing the main issues and problems involved in ring perception.
  • Downs, G.M. (1993) Rings - the importance of being perceived, In Chemical Structures 2, Warr, W.A. (Ed.), Springer-Verlag, Berlin, , pp. 207-219.
An updated review of the subject.
  • Downs, G.M. (1998) Ring Perception. In Encyclopedia of Computational Chemistry, Schleyer, P. von R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F.; Shreiner, P. R. (Eds.). Wiley, Chichester, 4, 2509-2515.
  • Downs, G.M. (2003) Ring Perception. In Handbook of Chemoinformatics, Gasteiger, J. (Ed.). Wiley-VCH, 1, 161-177.
 
Miscellaneous
This reference, a 'polemic', demonstrates that a previously proposed chemical reaction index based on the difference between reactant and product connectivity indices is unlikely to be useful.
  • Barnard, J.M.; Willett, P. (1981) Comments on a method for generating a chemical reaction index for storage and retrieval of information, J. Chem. Inf. Comput. Sci., 21, 140-141
The next three papers provide historical reviews of the then status of computerized chemical structure manipulation.
  • Barnard, J.M. (1983) Structural survey: ten years of chemical structure handling. Proceedings of the 10th Annual Conference, Hertford College, Oxford, July 1983. Association of Information Officers in the Pharmaceutical Industry (ISBN 0-9509165-01)
  • Barnard, J.M. (1984b) Computerised chemical information systems - do they really help? Summary, Proceedings of the CSA Seminar on Solving Chemical Problems, Imperial College London, April 14-15 1983. Chemical Structure Association 1984 (ISBN 0-947682-03-1)
  • Barnard, J.M. (1989b) Recent developments in chemical structure handling, In Perspectives in Information Management, Oppenheim, C.; Citroen, C.; Griffiths, J-M. (Eds.). Guildford: Butterworth Scientific.
See also
  • Barnard, J.M. (1994) Third International Conference on Chemical Structures, J. Chem. Inf. Comput. Sci., 34 (1) 1-2.
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