Genetic Algorithms and Protein Folding

by Dr. Steffen Schulze-Kremer
Westfälische Strasse 56, D-10711 Berlin, FRG
E-mail: steffen@chemie.fu-berlin.de
A collection of articles that use genetic algorithms for / in biocomputing.
References
  1. J. Holland, Genetic algorithms and the optimal allocations of trials, SIAM Journal of Computing, vol 2, no 2, pp. 88 - 105, 1973.
  2. I. Rechenberg, Bioinik, Evolution und Optimierung, Naturwissenschaftiche Rundschau, vol 26, pp. 465 - 472, 1973.
  3. J. Koza, Genetic Programming, MIT Press, 1993.
  4. S. Kirkpatrick, C. D. Gelatt, Jr., M. P. Vecchi, Optimization by Simulated Annealing, Science, vol 220, no 4598, pp. 671-680, 1983.
  5. T. Jones, S. Forrest, An Introduction to SFI Echo, November 1993, Santa Fe Institute, 1660 Old Pecos Trail, Suita A, Santa Fe NM 87501, email terry@sanatfe.edu, forrest@cs.unm.edu. World Wide Web Server at ftp://alife.santafe.edu/pub/SOFTWARE.
  6. J. H. Holland, Echoing Emergence: Objectives, Rough Definitions and Speculations for Echo-class Models, in Integrative Themes, (G. Cowan, D. Pines, D. Melzner, Eds.), Santa Fe Institute Studies in the Science of Complexity, Proc. Vol XIX, Reading, MA, Addison-Wesley, 1993.
  7. J. H. Holland, Adaptation in Natural and Artificial Systems, 2nd Ed., MIT Press, 1992.
  8. L. Davis, (ed.) Handbook of Genetic Algorithms, Van Nostrand Reinhold, New York, 1991.
  9. D. E. Goldberg, Genetic Algorithms in Search, Optimization & Machine Learning, Addison-Wesley, 1989.
  10. I. Rechenberg, Evolutionsstrategie, Frommann-Holzboog, Stuttgart, 1973, 2nd Edition 1994.
  11. H.-P. Schwefel, Numerical Optimization Of Computer Models, Chichester, John Wiley, 1981, (originally published in 1977).
  12. World Wide Web Servers with more information and software at
    http://lautaro.fb10.tu-berlin.de, http://www.cis.ohio-state.edu/hypertext/faq/usenet/ai-faq/genetic/top.html and
    http://www-mitpress.mit.edu/jrnls-catalog/evolution.html.
  13. G. E. Schulz, R. H. Schirmer, Principles of Protein Structure, Springer Verlag, 1979.
  14. A. M. Lesk, Protein Architecture - A Practical Approach, IRL Press, 1991.
  15. C. Branden, J. Tooze, Introduction to Protein Structure, Garland Publishing New York, 1991.
  16. S. Schulze-Kremer, Genetic Algorithms for Protein Tertiary Structure Prediction, in Parallel Problem Solving from Nature II, (R. Männer, B. Manderick, eds.), North Holland, pp. 391-400, 1992.
  17. For more information or to get in touch with researchers using genetic algorithms send an email to one of the following mailing lists: ga-molecule@interval.com, ga-list-request@aic.nrl.navy.mil or to Melanie Mitchell at mm@santafe.edu who keeps an extensive bibliography on applications of genetic algorithms in chemistry. Alternatively, try a search for „genetic algorithm“ in gopher space, for example at gopher://veronica.sunet.se.
  18. T. Dandekar, P. Argos, Potential of genetic algorithms in protein folding and protein engineering simulations, Protein Engineering, vol 5, no 7, pp. 637-645, 1992.
  19. S. M. Le Grand, K. M. Merz, The application of the genetic algorithm to the minimization of potential energy functions, The Journal of Global Optimization, vol 3, pp.49-66, 1993.
  20. S. Sun, Reduced representation model of protein structure prediction: statistical potential and genetic algorithms, Protein Science, vol 2, no 5, pp. 762-785, 1993.
  21. T. Dandekar, P. Argos, Folding the Main Chain of Small Proteins with the Genetic Algorithm, Journal of Molecular Biology, vol 236, pp. 844-861, 1994.
  22. r.m.s. = root mean square deviation; two conformations are superimposed and the square root is calculated from the sum of the squares of the distances between corresponding atoms.
  23. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi, The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures, Journal of Molecular Biology, 112, pp. 535-542, 1977.
  24. J. G. Vinter, A. Davis, M. R. Saunders, Strategic approaches to drug design. An integrated software framework for molecular modelling, Journal of Computer-Aided Molecular Design, vol 1, pp. 31-51, 1987.
  25. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, Charmm: A program for Macromolecular Energy, Minimization and Dynamics Calculations, Journal of Computational Chemistry, vol 4, no 2, pp. 187-217, 1983.
  26. J. T. Ngo, J. Marks, Computational complexity of a problem in molecular-structure prediction, Protein Engineering, vol 5, no 4, pp. 313-321, 1992.
  27. L. Davis, (ed.) Handbook of Genetic Algorithms, van Nostrand Reinhold, New York, 1991.
  28. C. B. Lucasius, G. Kateman, Application of Genetic Algorithms to Chemometrics, Proceedings 3rd International Conference on Genetic Algorithms, (J. D. Schaffer , ed.), Morgan Kaufmann Publishers, San Mateo, CA, pp. 170-176, 1989.
  29. P. Tuffery, C. Etchebest, S. Hazout, R. Lavery, A new approach to the rapid determination of protein side chain conformations, J. Biomol. Struct. Dyn., vol 8, no 6, pp. 1267-1289, 1991.
  30. W. A. Hendrickson, M. M. Teeter, Structure of the Hydrophobic Protein Crambin Determined directly from the Anomalous Scattering of Sulphur, Nature, vol 290, pp. 107, 1981.
  31. C. Lee, S. Subbiah, Prediction of protein side chain conformation by packing optimization, Journal of Molecular Biology, no 217, pp. 373-388, 1991.
  32. P. Tuffery, C. Etchebest, S. Hazout, R. Lavery, A new approach to the rapid determination of protein side chain conformations, J. Biomol. Struct. Dyn., vol 8, no 6, pp. 1267-1289, 1991.
  33. S. Schulze-Kremer, A. Levin, Search for Protein Conformations with a Parallel Genetic Algorithm: Evaluation of a Vector Fitness Function, Final Report and Technical Documentation of Protein Folding Application (Work package 1), European ESPRIT project # 6857 PAPAGENA, August 1994.
  34. N. M. Maiorov, G. M. Crippen, Contact potential that recognizes the correct folding of globular proteins, Journal of Molecular Biology, vol 227, pp. 876 - 888, 1992.
  35. N. Go, H. A. Scheraga, Ring Closure and Local Conformational Deformations of Chain Molecules, Macromolecules, vol 3, pp. 178-187, 1970.
  36. Quantum Chemical Exchange Program (QCEP) program No. QCMP 046.
  37. Intel Paragon with 98 x i860 processors owned by Parallab, University of Bergen, Norway.
  38. S. Y. Lu, K. S. Fu, A sentence-to-sentence clustering procedure for pattern analysis, IEEE Transactions on Systems, Man and Cybernatics SMC, vol 8, pp. 381 - 389, 1978.
  39. B. Rost, C. Sander, Prediction of protein secondary structure at better than 70% accuracy, Journal of Molecular Biology, vol 232, pp. 584 - 599, 1993.
  40. R.S. Cármenes, J.P. Freije, M.M. Molina, J.M. Martín, PREDICT7, a program for protein structure prediction, Biochem. Biophys. Res. Comm., vol 159, pp. 687-693, 1989.
  41. J. Garnier, D. J. Osguthorpe, B. Robson, Journal of Molecular Biology, vol 120, pp. 97-120, 1978.
  42. This is only available for test runs with already known protein conformations.