Stephen R. Heller
Abstract: In the past two years a number of PC based computer programs have been developed to allow one to perform chemical substructure searching on PC computers. This overview of the field will describe the features of five major systems, ChemBase, ChemSmart, chemFile, HTSS, and PSIGen/PSIBase.
1 INTRODUCTION
1. ChemBase
2. chemFile
3. ChemSmart
4. HTSS
5. PSIGen/PSIBase
That is, what purpose do these programs serve, and how can they be used in your environment?
2 CHEMBASE
3 CHEMFILE
4 CHEMSMART
5 HTSS
6 PSIGen/PSIBase
7 COMPARISON OF FEATURES
Templates Enlarge/Shrink Rotate Clean Valence Check
ChemBase Y Y Y Y Y
chemFile Y Y N N N
ChemSmart Y Y Y* N N
HTSS Y Y Y N Y
PSIGen/PSIBase Y Y Y N Y
* Rotation is by 90 degrees only
Exact Sub Max Size File
Structure Structure (Practical) Structure
ChemBase Y Y 4000 Sequential
chemFile Y Y 1000 Sequential
ChemSmart Y Y 2000 Sequential
HTSS Y Y 25000 Inverted Tree
PSIGen/PSIBase Y Y 6000 Primarily
Sequential
Text Interface to Interface to
PC DBMS Word Processor
ChemBase Y Y Y
chemFile Y N N
ChemSmart Name & MF* N N
HTSS N Y Y
PSIGen/PSIBase Name Only Y Y
(using PSICard)
* MF = Molecular Formula
ID # Name MF MW* Other Data
Fields
ChemBase Y Y Y Y Y
chemFile Y Y Y Y Y
ChemSmart Y Y Y N Y
HTSS Y N N N N
PSIGen/PSIBase Y Y N Y Y
* MW = Molecular Weight
Prices:
ChemBase $ 3500
chemFile $ 150
ChemSmart $ 335
HTSS $ 499
PSIGen/PSIBase $ 990
(PSICard, a program module which enables data and/or text to be stored and associated with a given chemical structure costs an additional $195).
8 SUMMARY
9 ACKNOWLEDGEMENTS
Stephen R. Heller
U.S. Department of Agriculture
Model and Database Coordination Laboratory
Building 007, Room 56, BARC-West
Beltsville, MD 20705-2350 USA
Phone: (301) 344-1709
Telemail: SRHELLER
Bitnet: SRHELLER @ ARS BARC
10 REFERENCES
1. Health Designs, Inc., 183 Main Street, Rochester, NY 14604 USA.
2. D. E. Meyer, "Microcomputer-Based Software for Chemical Structure Management: A Comparison", Chapter 4, pages 29-36, ACS Symposium Series #341, ACS, Washington DC 20036 USA, 1987.
3. W. Warr, "Introduction to Graphics for Chemical Structures", pages ix - xiii, ACS Symposium Series #341, ACS, Washington, DC 20036 USA, 1987.
4. Molecular Design Ltd., 2132 Farallon Drive, San Leandro, CA 94577 USA.
5. D. Meyer and Peter Cohan, "Designing New Compounds with a PC Database", Am. Biotech. Lab., 5(1), pages 32-39(1987).
6. C. Seiter, "Your PC May Solve Your Chem Lab Problems", R&D, 29(3), pages 94-96(1987).
7. B. Curry-Koenig, "PC Chemical Databases - New Tools for Chemists", Am. Clin. Prod. Rev., pages 10-17, March 1986.
8. COMPress, PO Box 102, Wentworth, NH 03282 USA.
9. J. Figueras, "An Electronic Notebook", Chapter 5, pages 37-47, ACS
Symposium Series #341, ACS, Washington DC 20036 USA, 1987.
10. ISI Software, ISI, 3501 Market Street, Philadelphia, PA 19104 USA.
11. S. R. Gould and D. E. Meyer, "A Chemical Management Systems for Microcomputers", Amer. Lab., 19 (3), 126-127(1987).
12. D. E. Meyer, "Software for Accessing Chemical Information", Amer. Lab., 19(6), 124-125(1987).
13. Z. M. Nagy, T. Veszpremi, G. Csonka, and P. Bruck, "Substructure Search on a Hierarchic Tree of Chemical Graphs", in S. R. Heller and R. Potenzone (Eds.), Computer Applications in Chemistry, Proceedings of the 6th International Conference on Computers in Chemical Research and Education, pages 335-336, Elsevier Science Publishers, Amsterdam (1983).
14. HTSS (also known as TREE), Technical Data Service (TDS) Inc., Suite 2300, 10 Columbus Circle, New York, NY 10019 USA.
15. Hampden Data Services Ltd., Hampden Cottage, Abingdon Road, Clifton Hampden, Abingdon, Oxon, OXC14 3EG, England.
16. R. E. Feldmann and S. R. Heller, "An Application of Interactive Graphics - The Nested Retrieval of Chemical Structures", J. Chem. Doc., 12, 48-54(1972).
17. Markush formulas are generic chemical structures, typically characterized by having variable nature substituent groups and variable substitution patterns on chains of atoms and rings. For example see V. J. Gillet, S. M. Welford, M. F. Lynch, P. Willett, J. M. Barnard, and G. M. Downs, "Computer Storage and Retrieval of Generic Chemical Structures in Patents. 7. Parallel Simulation of a Relation Algorithm for Chemical Substructure Search", J. Chem. Inf. Comput. Sci., 26, pages 126-130(1986) and references cited therein.