Bioinformatics

Speaker Jim Golden William Hart

Affiliation Computational Biology Coordinator, Pioneer Hi-Bred Intl. Sandia National Labs.

Seminar title Complex Adaptive Systems in Bioinformatics Hybrid Evolutionary Methods for Molecular Structure Prediction: Combining Global and Local Search

Links

Pioneer Hi-Bred International, Inc.
Chaos Games and Genetics
Mining the Genome

AutoDock
Memetic algorithms (hybrid evolutionary algorithms)
Sandia Optimization Web Page
Computational Biology at Sandia National Labs
The Tortilla Project - Ab Inito Protein Folding

Readings

H. Joel Jeffrey (1990) Chaos game representation of gene structure. Nucleic Acids Research, Vol. 18, No. 8. pp. 2163-2170
V. Solovyev, S. Korolev, H. Lim (1993) A new approach for the classification of functional regions of DNA sequences based on fractal representation. Int. Journal of Genome Research, Vol. 1. No. 2. pp. 109-128.
W. Li, T. Marr, K. Kaneko (1994) Understanding long-range correlations in DNA sequences. Physica D. 75. pp. 392-416.
H. Herzel, E. Trifonov, O. Weiss, I. Grosse (1998) Interpreting correlations in biosequences. Physica A. 249. pp. 449-459.

Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function, G M Morris, D S Goodsel, R S Halliday, R Huey, W E Hart, R K Belew, and A J Olson. J Comp Chem. 19(14):1639-1662. 1998.
Goodsell, D. S., Morris, G. M. and Olson, A. J. (1996), J. Mol. Recognition, 9: 1-5. "Docking of Flexible Ligands: Applications of AutoDock".
Improved Evolutionary Hybrids for Flexible Ligand Docking in Autodock, W E Hart, C R Rosin, R K Belew, G M Morris. Proc Intl Conf on Optimization in Computational Chem and Molec Bio. (to appear). 1999.

Speaker	Jim Golden	William Hart
Affiliation	Computational Biology Coordinator, Pioneer Hi-Bred Intl.	Sandia National Labs.
Seminar title	Complex Adaptive Systems in Bioinformatics	Hybrid Evolutionary Methods for Molecular Structure Prediction: Combining Global and Local Search
Links	Pioneer Hi-Bred International, Inc. Chaos Games and Genetics Mining the Genome	AutoDock Memetic algorithms (hybrid evolutionary algorithms) Sandia Optimization Web Page Computational Biology at Sandia National Labs The Tortilla Project - Ab Inito Protein Folding
Readings	H. Joel Jeffrey (1990) Chaos game representation of gene structure. Nucleic Acids Research, Vol. 18, No. 8. pp. 2163-2170 V. Solovyev, S. Korolev, H. Lim (1993) A new approach for the classification of functional regions of DNA sequences based on fractal representation. Int. Journal of Genome Research, Vol. 1. No. 2. pp. 109-128. W. Li, T. Marr, K. Kaneko (1994) Understanding long-range correlations in DNA sequences. Physica D. 75. pp. 392-416. H. Herzel, E. Trifonov, O. Weiss, I. Grosse (1998) Interpreting correlations in biosequences. Physica A. 249. pp. 449-459.	Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function, G M Morris, D S Goodsel, R S Halliday, R Huey, W E Hart, R K Belew, and A J Olson. J Comp Chem. 19(14):1639-1662. 1998. Goodsell, D. S., Morris, G. M. and Olson, A. J. (1996), J. Mol. Recognition, 9: 1-5. "Docking of Flexible Ligands: Applications of AutoDock". Improved Evolutionary Hybrids for Flexible Ligand Docking in Autodock, W E Hart, C R Rosin, R K Belew, G M Morris. Proc Intl Conf on Optimization in Computational Chem and Molec Bio. (to appear). 1999.