Chemical information in 3D space

Journal of Chemical Information and Computer Sciences

Volumn 36, Issue 5, 1996, Pages 1030-1037

  Gasteiger, Johann ^a   Sadowski, Jens ^a   Schuur, Jan ^a   Selzer, Paul ^a   Steinhauer, Larissa ^a   Steinhauer, Valentin ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000405995     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci960343+     Document Type: Article

References (46)

1. Jochum, C.; Gasteiger, J. Canonical Numbering and Constitutional Symmetry. J. Chem. Inf. Comput. Sci. 1977, 17, 113-117.
2. Carhart, R. E. Erroneous Claims Concerning the Perception of Topological Symmetry. J. Chem. Inf. Comput. Sci. 1978, 18, 108-109.
3. Jochum, C.; Gasteiger, J. On the Misinterpretation of Our Algorithm for the Perception of Constitutional Symmetry. J. Chem. Inf. Comput. Sci. 1979, 19, 49-50.
4. Carfiart, R. E. Perception of Topological Symmetry. J. Chem. Inf. Comput. Sci. 1979, 19, 56.
5. Dyott, T. M.; Howe, W. J. Canonical Numbering, J. Chem. Inf. Comput. Sci. 1979, 19, 187.
6. Sadowski, J.; Gasteiger, J. From Atoms and Bonds to Three-dimensional Atomic Coordinates: Automatic Model Builders. Chem. Rev. 1993, 93, 2567-2581.
7. Luckenbach, R. Dynamic Stereochemistry of Pentaco-ordinaled Phosphorus and Related Elements; Georg Thieme Publishers: Stuttgart, 1973.
8. Gasteiger, J. A. Representation of Pi-Systems for Efficient Computer Manipulation. J. Chem. Inf. Comput. Sci. 1979, 19, 111-115.
9. Welford, S. M. In Software - Entwicklung in der Chemie 1'. Gasteiger, J. Ed.; Springer: Berlin, 1987: pp 5-11.
10. Bauerschmidt, S.; Gasteiger, J. Unpublished results.
11. Alien, F. H.; Davies, J. E.; Galloy, J. J.; Johnson, O.; Kennard, O.; Macrae, C. F.; Smith, J. M.; Watson, D. G. The Development of Version 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 1991, 31, 187-204.
12. Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of Automatic Three Dimensional Model Builders Using 639 X-Ray Structures. J. Chem. Inf. Comput. Sci. 1994, 34, 1000-1008.
13. Hiller, C.; Gasteiger, J. In Software Entwicklung in der Chemie 1: Gasteiger. J.; Ed.; Springer-Verlag: Berlin, 1987: pp 53-66.
14. Gasteiger, J.; Rudolph, C.; Sadowski, J. Automatic Generation of 3D a Atomic Coordinates for Organic Molecules. Tetrahedron Comput. Method. 1992, 3, 537-547.
15. Sadowski, J.; Rudolph, C.; Gasteiger, J. The Generation of 3D Models of Host - Guest Complexes. Anal. Chim. Acta 1992, 265, 233-241.
16. Sadowski, J.; Schwab, C.; Gasteiger, J. Unpublished results.
17. ALCOGEN is available from Chemical Concepts, Weinheim, Germany.
18. Davies, K.; Dunn, D.; Upton, R. An Algorithm to Generate 3D Structures from 2D Connection Tables; Poster on the 5th Molecular Modeling Workshop; Darmstadt, 1991.
19. (a) Leach, A. R.; Prout, K. Automated Conformational Analysis: Directed Conformational Search Using the A* Algorithm. J. Comput. Chem. 1990, 11, 1193-1205.
20. (b) Leach, A. R.; Smellie, A. S. A Combined Model-Building and Distance Geometry Approach to Automated Conformational Analysis and Search. J. Chem. Inf. Comput. Sci. 1992, 32, 379-385.
21. (c) COBRA is available from Oxford Molecular Ltd., Oxford, England.
22. (a) Rusinko, A., III. Tools for Computer-Assisted Drug Design. Ph.D. Thesis. University of Texas at Austin, Austin, TX, 1988.
23. (b) Pearlman, R. S. Rapid Generation of High Quality Approximate 3D Molecular Structures. Chem. Des. Auto. News 1987, 2, 1/5-6.
24. (c) Concord User's Manual; TRIPOS Associates: St Louis, MO, 1988.
25. (d) CONCORD is available from TRIPOS Associates.
26. Gordeeva, E. V.; Katrizky, A. R.; Shcherbukhin, V. V.; Zefirov, N. S. Rapid Conversion of Molecular Graphs to Three-dimensional Representation Using the MOLGEO Program. J. Chem. Inf. Comput. Sci. 1993, 33, 102-111.
27. CONVERTER, available from Biosym Technologies, San Diego, CA, U.S.A. We thank Dr. M. Waldman for providing us with the results of CONVERTER.
28. This kind of representation of the quantity-quality characteristics has been suggested by Dr. V. van Geerestein (AKZO Organon, Oss, The Netherlands).
29. Schuur, J. H.; Selzer, P.; Gasteiger, j. The Coding of the Three Dimensional Structure of Molecules by Molecular Transforms and Its Application to Structure - Spectra Correlations and Studies of Biological Activity. J. Chem. Inf. Comput. Sci. 1996, 36, 334-344.
30. Wierl, R. Elektronenbeugung und Molekülbau, Ann. Phys. (Leipzig) 1931, 8, 521-564.
31. Soltzberg, L. J.; Wilkins, C. L. Molecular Transforms: A Potential Tool for Structure Activity Studies. J. Am. Chem. Soc. 1977. 99, 439-443.
32. Gasteiger, J. Empirical Methods for the Calculation of Physicochemical Data of Organic Compounds. In Physical Property Prediction in Organic Chemistry; Jochum, C., Hicks, M. G., Sunkel, J., Eds.; Springer-Verlag: Heidelberg, 1988; pp 119-138.
33. Cramer, R. D., III: Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
34. Wagener, M.; Sadowski, J.; Gasteiger, J. Autocorrelation of Molecular Surface Properties for Modeling Corticosteroid Binding Globulin and Cytosolic Ah Receptor Activity by Neural Networks. J. Am. Chem. Soc. 1995, 117, 7769-7775.
35. The steroid structures can be retrieved by anonymous ftp: ftp:// cygnus.organik.uni-erlangen.de. login/ftp://cygnus.organik.uni-erlan-gen.de/pub/steroids/steroids.sd.
36. Gasteiger, J.; Marsili, M. Iterative Partial Equalization of Orbital Electronegativity - A Rapid Access to Atomic Charges. Tetrahedron 1980, 36, 3219-3228.
37. Gasteiger, J.; Saller, H. Calculation of the Charge Distribution in Conjugated Systems by a Quantification of the Resonance Concept. Angew. Chem. 1985, 97, 699-701; Angew. Chem., Int. Ed. Engl. 1985, 24, 687-689.
38. Gasteiger, J.; Saller, H. Calculation of the Charge Distribution in Conjugated Systems by a Quantification of the Resonance Concept. Angew. Chem. 1985, 97, 699-701; Angew. Chem., Int. Ed. Engl. 1985, 24, 687-689.
39. Kohonen, T. Self-Organisation and Associative Memory, 3rd ed.; Springer: Berlin, 1989.
40. Gasteiger, J.; Zupan, J. Neural Networks in Chemistry. Angew: Chem. 1993, 105, 510-536; Angew. Chem., Int. Ed. Engl. 1993, 32, 503-527.
41. Gasteiger, J.; Zupan, J. Neural Networks in Chemistry. Angew: Chem. 1993, 105, 510-536; Angew. Chem., Int. Ed. Engl. 1993, 32, 503-527.
42. Zupan, J.; Gasteiger, J. Neural Networks for Chemists - An introduction; VCH: Weinheim, 1993.
43. Hecht-Nielsen, T. Counterpropagation Networks. Applied Optics 1987, 26, 4979-4984.
44. SpecInfo, available from Chemical Concepts, Weinheim, Germany.
45. Novic, M.; Zupan, J. Investigation of Infrared Spectra-Structure Correlation Using Kohonen and Counterpropagation Network. J. Chem. Inf. Comput. Sci. 1995, 35, 454-466.
46. Steinhauer, L.; Steinhauer, V.; Gasteiger, J. Obtaining the 3D Structure from Infrared Spectra of Organic Compounds Using Neural Networks. In Software Development in Chemistry 10; Gasteiger, J., Ed.; Gesellschaft Deutscher Chemiker, Frankfurt am Main, Germany, 1996.