Comments on temporal logics for real-time system specification

ACM Computing Surveys

Volumn 41, Issue 2, 2009, Pages

  Furia, Carlo A ^a   Pradella, Matteo ^b   Rossi, Matteo ^a  

^a POLITECNICO DI MILANO   (Italy)

^b CNR   (Italy)

Author keywords

Temporal logic

Indexed keywords

REAL TIME SYSTEMS; SPECIFICATIONS; SURVEYS;

TEMPORAL LOGIC;

EID: 61949446035     PISSN: 03600300     EISSN: 15577341     Source Type: Journal    
DOI: 10.1145/1459352.1459358     Document Type: Article

References (75)

1. ADAM, D. 2002. Chemists synthesize a single naming system. Nature 417, 369.
2. BAJORATH, J., ED. 2004. Chemoinformatics: Concepts, Methods and Tools for Drug Discovery. Humana Press, Totowa, NJ.
3. BALABAN, A. T. 1985. Applications of graph theory in chemistry. J. Chem. Inf. Comput. Sci. 26, 334-343.
4. BARNARD, J. M. AND DOWNS, G. M. 1992. Clustering of chemical structures on the basis of two-dimensional similarity measures. J. Chem. Inf. Comput. Sci. 32, 644-649.
5. BAUERSCHMIDT, S. AND GASTEIGER, J. 1997. Overcoming the limitations of a connection table description: A universal representation of chemical species. J. Chem. Inf. Comput. Sci. 37, 705-714.
6. BEMIS, G. W. AND MURCKO, M. A. 1996. The properties of known drugs. 1. Molecular frameworks. J. Med. Chem. 39, 2887-2893.
7. BENDER, A. AND GLEN, R. C. 2004. Molecular similarity: A key technique in molecular informatics. Org. Biomol. Chem. 2, 3204-3218.
8. BÖHM, H.-J., FLOHR, A., AND STAHL, M. 2004. Scaffold hopping. Drug Discou. Today: Tech. 1, 217-224.
9. BROOIJMANS, N. AND KUNTZ, I. D. 2003. Molecular recognition and docking algorithms. Ann. Rev. Biophys. Biomol. Struct. 32, 335-373.
10. BROWN, F. K. 1998. Chemoinformatics: What is it and how does it impact drug discovery? Ann. Rep. Med. Chem. 33, 375-384.
11. BROWN, N. AND JACOBY, E. 2006. On scaffolds and hopping in medicinal chemistry. Mini Rev. Med. Chem. 6, 1217-1229.
12. BROWN, N. AND LEWIS, R. A. 2006. Exploiting QSAR methods in lead optimization. Curr. Opin. DrugDiscov. Devel. 9, 419-424.
13. BROWN, N., MCKAY, B., AND GASTEIGER, J. 2005. Fingal: A novel approach to geometric fingerprinting and a comparative study of its application to 3D QSAR modelling. QSAR Comb. Sci. 24, 480-484.
14. BROWN, N., MCKAY, B., GILARDONI, F., AND GASTEIGER, J. 2004. A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules. J. Chem. Inf. Comput. Sci. 44, 1079-1087.
15. BROWN, R. D. AND MARTIN, Y. C. 1997. The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 37, 1-9.
16. CECHETTO, J. D., ELOWE, N. H., BLANCHARD, J. E., AND BROWN, E. D. 2004. High-throughput screening at McMaster University: Automation in academe. J. Assoc. Lab. Auto. 9, 307-311.
17. COHEN, J. 2004. Bioinformatics-an introduction for computer scientists. ACM Comput. Surv. 36, 122-158.
18. COLES, S. J., DAY, N. E., MURRAY-RUST, P., RZEPA, H. S., AND ZHANG, Y. 2005. Enhancement of the chemical semantic web through the use of InChI identifiers. Org. Biomol. Chem. 3, 1832-1834.
19. COREY, E. J. AND CHENG, X.-M. 1995. The Logic of Chemical Synthesis. Wiley, New York, NY.
20. CRAMER, R. D., III., PATTERSON, D. E., AND BUNCE, J. D. 1988. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carried proteins. J. Amer. Chem. Soc. 110, 5959-5967.
21. CRUM BROWN, A. 1864. On the theory of isomeric compounds. Trans. Roy. Soc. Edinb. 23, 707-719.
22. CRUM BROWN, A. AND FRASER, T. R. 1869. V.-On the connection between chemical constitution and physiological action. Part. I.-On the physiological action of the salts of the ammonium bases, derived from strychnia, brucia, thebaia, codeia, morphia, and nicotia. Trans. Roy. Soc. Edinb. 25, 151-203.
23. DIESTEL, R. 2000. Graph Theory, 2nd Ed. Springer-Verlag, New York, NY.
24. DIMASI, J. A., HANSEN, R. W., AND GRABOWSKI, H. G. 2003. The price of innovation: New estimates of drug development costs. J. Health Econ. 22, 151-185.
25. DURANT, J. L., LELAND, B. A., HENRY, D. R., AND NOURSE, J. G. 2002. Reoptimization of MDL keys for use in drug discovery. J. Chem. Inf. Comput. Sci. 42, 1273-1280.
26. ERIKSSON, L., ARNHOLD, T., BECK, B., FOX, T., JOHANSSON, E., AND KRIEGL, J. M. 2004. Onion design and its application to a pharmaceutical QSAR problem. J. Chemomet. 18, 188-202.
27. ERIKSSON, L., JAWORSKA, J., WORTH, A. P., CRONIN, M. T. D., AND MCDOWELL, R. M. 2003. Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs. Environ. Health Perspect. 111, 1361-1375.
28. ERTL, P 2007. In silico identification of bioisosteric functional groups. Curr. Opin. DrugDiscov. Devel. 10, 281-288.
29. FERRARA, P., PRIESTLE, J. P., VANGREVELINGHE, E., AND JACOBY, E. 2006. New developments and applications of docking and high-throughput docking for drug design and in silico screening. Curr. Comp.-Aided Drug Des. 2, 83-91.
30. FUJITA, T., IWASA, J., AND HANSCH, C. 1964. A new substituent constant, π, derived from partition coefficients. J. Amer. Chem. Soc. 86, 5175-5180.
31. GASTEIGER, J., ED. 2003. The Handbook of Chemoinformatics. Wiley-VCH, Weinheim, Germany.
32. GASTEIGER, J. AND ENGEL, T., EDS. 2003. Chemoinformatics: A Textbook. Wiley-VCH, Weinheim, Germany.
33. GASTEIGER, J., PFÖRTNER, M., SITZMANN, M., HÖLLERING, R., SACHER, O., KOSTKA, T., AND KARG, N. 2000. Computer-assisted synthesis and reaction planning in combinatorial chemistry. Persp. DrugDiscov. Des. 20, 1-21.
34. GASTEIGER, J., RUDOLPH, C., AND SADOWSKI, J. 1990. Automatic generation of 3D atomic coordinates for organic molecules. Tetrahed. Comput. Methodol. 3, 537-547.
35. GHOSE, A. K. AND CRIPPEN, G. M. 1986. Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity. J. Comp. Chem. 7, 565-577.
36. GILLET, V. J., WILLETT, P., BRADSHAW, J., AND GREEN, D. V. S. 1999. Selecting combinatorial libraries to optimize diversity and physical properties. J. Chem. Inf. Comput. Sci. 39, 169-177.
37. GOLDBERG, K., NEWMAN, M., AND HAYNSWORTH, E. 1972. Combinatorial Analysis. In Handbook of Mathematical Functions With Formulas, Graphs, and Mathematical Tables, 10th ed. Abramowitz, M., Stegun, I. A. Eds. U.S. Government Printing Office: Washington, DC, 824-825.
38. GORSE, A.-D. 2006. Diversity in medicinal chemistry space. Curr. Top. Med. Chem. 6, 3-18.
39. GUND, P. 1979. Pharmacophore pattern searching and receptor mapping. Ann. Rep. Med. Chem. 14, 299-308.
40. GÜNER, O. F. 2005. The impact of pharmacophore modeling in drug design. IDrugs 8, 567-572.
41. HASTIE, T., TIBSHIRANI, R., AND FRIEDMAN, J. 2001. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. Springer-Verlag, New York, NY.
42. HERT, J., WILLETT, P., WILTON, D. J., ACKLIN, P., AZZAOUI, K., JACOBY, E., AND SCHUFFENHAUER, A. 2004. Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J. Chem. Inf. Comput. Sci. 44, 1177-1185.
43. JOHNSON, M. A. AND MAGGIORA, G. M. Eds. 1990. Concepts and Applications of Molecular Similarity. Wiley Inter-Science, New York, NY.
44. JONES, G., WILLETT, R. GLEN, R. C., LEACH, A. R., AND TAYLOR, R. 1997. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727-748.
45. KARELSON, M. 2000. Molecular Descriptors in QSAR/QSPR. Wiley-VCH, Weinheim, Germany.
46. KITCHEN, D. B., DECORNEZ, H., FURR, J. R., AND BAJORATH, J. 2004. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Rev. Drug Discov. 3, 935-949.
47. KUNTZ, I. D., BLANEY, J. M., OATLEY, S. J., LANGRIDGE, R., AND FERRIN, T. E. 1982. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288.
48. LEACH, A. R. 2001. Molecular Modelling: Principles and Applications, 2nd ed. Prentice Hall, Harlow, U.K.
49. LEACH, A. R. AND GILLET, V J. 2003. An Introduction to Chemoinformatics. Kluwer Academic Publishers, Dordrecht, The Netherlands.
50. LEWELL, X. Q., JUDD, D. B., WATSON, S. P., AND HANN, M. M. 1998. RECAP-retrosynthetic analysis procedure: A powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci. 38, 511-522.
51. LIPINSKI, C. A., LOMBARDO, F., DOMINY, B. W., AND FEENEY, P. J. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46, 3-26.
52. LIVINGSTONE, D. J. 2000. The characterization of chemical structures using molecular properties. A survey. J. Chem. Inf. Comput. Sci. 40, 195-209.
53. LYNCH, M. F. 2004. Introduction of computers in chemical structure information systems, or what is not recorded in the annals. In The History and Heritage of Scientific and Technological Information Systems: Proceedings of the 2002 Conference, W. B. Rayward and M. E. Bowden, Eds. Information Today, Inc., Medford, NJ, 137-148.
54. MARKUSH, E. A. 1924. Pyrazolone dye and process of making the same. U.S. Patent No. 1,506,316, August 26.
55. MIGLIAVACCA, E. 2003. Applied introduction to multivariate methods used in drug discovery. Mini Rev. Med. Chem. 3, 831-843.
56. MORGAN, H. L. 1965. The generation of a unique machine description for chemical structures - a technique developed at chemical abstracts service. J. Chem. Doc. 5, 107-113.
57. NICOLAOU, C. A., BROWN, N., AND PATTICHIS, C. S. 2007. Molecular optimization using multi-objective methods. Curr. Opin. DrugDiscov. Devel. 10, 316-324.
58. OPREA, T. Ed. 2005a. Chemoinformatics in Drug Discovery. Wiley-VCH, Weinheim, Germany.
59. OPREA, T. 2005b. Is safe exchange of data possible? Chem. Eng. News 83, 24-29.
60. PEARLMAN, R. S. 1987. Rapid generation of high quality approximate 3D molecular structures. Chem. Des. Automa. News 2, 5-7.
61. RAEVSKY, O. A. 2004. Physicochemical descriptors in property-based drug design. Mini Rev. Med. Chem. 4, 1041-1052.
62. REICH, H. J. AND CRAM, D. J. 1969. Macro rings. XXXVII. Multiple electrophilic substitution reactions of [2,2]paracyclophanes and interconversions of polysubstituted derivatives. J. Am,. Chem,. Soc. 91, 3527-3533.
63. ROGERS, D., BROWN, R. D., AND HAHN, M. 2005. Using extended-connectivity fingerprints with Laplacianmodified Bayesian analysis in high-throughput screening follow-up. J. Biomol. Screen. 10, 682-686.
64. RUSSO, E. 2002. Chemistry plans a structural overhaul. Nature Jobs 419, 4-7.
65. SCHNEIDER, G. AND FECHNER, U. 2005. Computer-based de novo design of drug-like molecules. Nature Rev. DrugDiscov. 4, 649-663.
66. SCHUPPENHAUER, A. AND BROWN, N. 2006. Chemical diversity and biological activity. Drug Discov. Today: Technol. 3, 387-395.
67. SCHUFFENHAUER, A., BROWN, N., SELZER, P., ERTL, P., AND JACOBY, E. 2006. Relationships between molecular complexity, biological activity, and structural activity. J. Chem. Inf. Mod. 46, 525-535.
68. SCHUFFENHAUER, A., FLOERSHEIM, P., ACKLIN, P., AND JACOBY, E. 2003. Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci. 43, 391-405.
69. SCHUFFENHAUER, A., BROWN, N., ERTL, P., JENKINS, J. L., SELZER, P., AND HAMON, J. 2007. Clustering and rulebased classifications of chemical structures evaluated in the biological activity space. J. Chem. Inf. Mod. 47, 325-336.
70. SNAREY, M., TERRETT, N. K.,WILLETT, P., ANDWILTON, D. J. 1997. Comparison of algorithms for dissimilaritybased compound selection. J. Mol. Graph. Mod. 15, 372-385.
71. TODESCHINI, R. AND CONSONNI, V. 2000. Handbook of Molecular Descriptors. Wiley-VCH, Weinheim, Germany.
72. WEININGER, D. 1988. Smiles a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28, 31-36.
73. WILLETT, P. 1991. Three-Dimensional Chemical Structure Handling. Research Studies Press, Balclock, Hertfordshine, U.K.
74. WILLETT, P. 2000. Textual and chemical information processing: Different domains but similar algorithms. Inform. Res. 5, http://informationr.net/ir/5-2/paper69.html.
75. WILLETT, P., BARNARD, J. M., AND DOWNS, G. M. 1998. Chemical similarity searching. J. Chem. Inf. Comput. Sci. 38, 983-996.