 |
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| ... Publications
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This
page lists publications by Digital Chemistry Directors
and 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.
We have divided these into themed categories
and annotated with further detail for your convenience,
some papers will appear in more than one category. |
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| 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. |
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|
- 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.
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| 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.
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| |
| 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. |
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|
- 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.
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| 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.
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| 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.
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| 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
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| 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
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| 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.
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| |
| 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.
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|
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
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| 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
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| |
| 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). |
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|
- 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.
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| 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.
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| 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
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| 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.
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| 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. |
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|
- 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
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| 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.
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| 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
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| 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
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| 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.
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| |
| 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. |
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|
- 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
last 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.
|
| |
| 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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