Applications of genetic algorithms in molecular diversity

Current Opinion in Chemical Biology

Volumn 2, Issue 3, 1998, Pages 381-385

  Weber, Lutz ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DARWINIA;

PEPTIDE; PEPTIDE LIBRARY;

ALGORITHM; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMISTRY; CONSENSUS SEQUENCE; DRUG DESIGN; EVOLUTION; METHODOLOGY; ORGANIC CHEMISTRY; REVIEW; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; AMINO ACID SEQUENCE; CHEMISTRY, ORGANIC; CONSENSUS SEQUENCE; DRUG DESIGN; EVOLUTION; MODELS, GENETIC; PEPTIDE LIBRARY; PEPTIDES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0032087817     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(98)80013-6     Document Type: Article

References (28)

1. Cook WJ, Cunningham WH, Pulleyblank WR, Schrijver A: Combinatorial Optimization. New York: Wiley and Sons Inc; 1997.
2. Holland JH: Adaptation in Natural and Artificial Systems. Cambridge: MIT Press; 1992.
3. Forrest M, Mitchell M: Foundations of Genetic Algorithms 2. Edited by Whitley D. San Mateo: Morgan Kaufmann; 1996.
4. Rechenberg I: Evolutionsstrategie '94. Stuttgart: Frommann-Holzboog; 1994.
5. Ugi I, Bauer J, Bley K, Dengler A, Dietz A, Fontain E, Gruber B, Herges R, Knauer M, Reitsam K, Stein N: Computer-assisted solution of chemical problems-the historical development and the present state of the art of a new discipline of chemistry. Angew Chem Int Ed 1993, 32:201-227.
6. Weiniger D: SMILES: a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inform Comput Sci 1988, 28:31-36.
7. Venkatasubramanian V, Chan K, Caruthers J: Evolutionary design of molecules with desired properties using the genetic algorithm. J Chem Inform Comput Sci 1995, 35:188-195.
8. Glen RC, Payne AWR: A genetic algorithm for the automated generation of molecules within constraints. J Comput Aided Mol Des 1995, 9:181-202.
9. Weber L, Wallbaum S, Broger C, Gubernator K: A genetic algorithm optimizing biological activity of combinatorial compound libraries. Angew Chem Int Ed 1995, 107:2453-2454.
10. Brown RD, Martin YC: Designing combinatorial library mixtures using a genetic algorithm. J Med Chem 1997, 40:2304-2313.
11. Sheridan RP, Kearsley SK: Using a genetic algorithm to suggest combinatorial libraries. J Chem Inform Comput Sci 1995, 35:310-320.
12. James CA, Weiniger D; Daylight Theory Manual. Irvine: Daylight Chemical Information Systems Inc; 1995.
13. Ugi I, Wochner M, Fontain E, Bauer J, Gruber B, Karl R: Chemical similarity, chemical distance and computer assisted formalized reasoning by analogy. In Concepts and Applications of Molecular Similarity. Edited by Johnson MA, Maggiora GM. New York: Wiley & Sons Inc; 1990:239-288.
14. Schneider G, Grunert HP, Schuchhardt J, Wolf K-U, Müller G, Habermehl K-O, Zeichhardt H, Wrede P: A peptide selection scheme for systematic evolutionary design and construction of synthetic peptide libraries. Minimal Invasive Medizin 1995, 6:106-115.
15. Shemetulskis NE, Weiniger D, Blankley CJ, Yang JJ, Humblet C: Stigmata: an algorithm to determine structural commonalities in diverse datasets. J Chem Inform Comput Sci 1996, 36:862-871.
16. King RD, Muggleton S, Lewis RA, Sternberg MJE: Drug design by machine learning: the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase. Proc Natl Acad Sci USA 1992, 89:11322-11326.
17. King RD, Muggleton S, Srinivasan A, Sternberg MJE: Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming. Proc Natl Acad Sci USA 1996, 93:438-442.
18. So S-S, Karplus M: Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural networks. J Med Chem 1996, 39:1521-1530.
19. So S-S, Karplus M: Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 1. Method and validations. J Med Chem 1997, 40:4347-4359.
20. So S-S, Karplus M: Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 2. Applications. J Med Chem 1997, 40:4360-4371.
21. Brown RD, Martin YC: Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J Chem inform Comput Sci 1996, 36:572-584. Describes and evaluates different clustering methods using various parameter sets to select representative sublibraries of large compound libraries.
22. Shemetulskis NA, Dunbar JB Jr, Dunbar BW, Moreland DW, Humblet C: Enhancing the diversity of a corporate database using chemical clustering and analysis. J Comput Aided Mol Des 1995, 9:407-416.
23. Martin EJ, Blaney JM, Siani MA, Spellmeyer DC, Wong AK, Moos WH: Measuring diversity: experimental design of combinatorial libraries for drug discovery. J Med Chem 1995, 38:1431-1436.
24. Yokobayashi Y, Ikebukuro K, McNiven S, Karube I: Directed evolution of trypsin inhibiting peptides using a genetic algorithm. J Chem Soc Perkin Trans I 1996, 2435-2437. A hexapeptide library is optimised for trypsin inhibition in six cycles of synthesis and screening.
25. Singh J, Ator MA, Jaeger EP, Allen MP, Whipple DA, Soloweij JE, Chowdhary S, Treasurywala AM: Application of genetic algorithms to combinatorial synthesis: a computational approach to lead identification and lead optimization. J Am Chem Soc 1996, 118:1669-1676. Stromelysin inhibitors are evolved from hexapeptides by a genetic algorithm in five generations.
26. Schneider G, Hahn U, Fatemi A, Müller G, Wrede P: Peptide design in machina: artificial signal peptidase I cleavage-sites are processed in vivo. Minimal Invasive Medizin 1995, 6:72-77.
27. Wrede P, Klages S, Landt O, Hahn U, Schneider G: Peptide design aided by neural networks: biological activity of artificial signal peptidase I cleavage sites. Biochemistry 1998, 37:3588-3593.
28. Devillers J (Ed): Genetic Algorithms In Molecular Modeling. London: Academic Press; 1996.