Subject: Seeking Information about Genetic Algorithms

From: [email-masked]
Date: Sat, 28 Aug 1993 15:53 -0400 (EDT)

Dear Netters:
Not very much has been published on GA applications in
physical sciences or chemistry or related disciplines.
I am looking for recent papers or work in progress using
GA in chemistry. Do you know of such work? Could you please
pass along any information you  have? Thanks for the help.
Peter Jurs, Penn State University Chemistry Department
[email-masked]

---

From: "Leon Y. Xiao, (502)635-6931" <[email-masked]>
Date: Sat, 28 Aug 1993 22:19:19 -0500 (EST)

Hi, Peter:

In your mail,

>Peter Jurs, Penn State University Chemistry Department

Following is a list of publications (most, but not limited)
you may be interested in.

Leon Xiao
University of Louisville
Chemistry Department

==============================================================

[BOOKS]

Holland, J. H. Adaptation in natural and artificial systems: an
introductory analysis with applications to biology, control, and
artificial intelligence. University of Michigan Press, Ann Arbor, 
MI. (1975). 

Davis, L. Genetic Algorithms and simulated annealing. Morgan
Kaufmann Publishers, Los Altos, CA.(1987). 

Goldberg, D. E. Genetic algorithms in search, optimization, and
machine learning, Addision-Wesley, New York. (1989).

Davis, L. Handbook of genetic algorithms. Van Nostrand Reinhold,
NY. (1991).

Z. Michalewicz, Springer Verlag Genetic algorthms + Data Structures =
evolution programs; (1992).

[CONFERENCE PROCEEDINGS]

Grefenstette, J. J. Genetic algorithms and their applications:
proceeding of the second International Conference on Genetic
Algorithms. L. Erlbaum Associates, Hillsdale, NJ. (1987).

Schaffer, J. D. Proceedings of the Third International Conference
on Genetic Algorithms. Morgan Kaufmann Publishers, San Mateo, CA.(1989). 

Belew, R. K. and Booker, L. B. Proceedings of the Fourth
International Conference on Genetic Algorithms. Morgan Kaufmann
Publishers, San Mateo, CA. (1991).

Forest, S. ed., Proceedings of the Fifth International Conference on
Genetic  Algorithms, Morgan Kaufmann Publishers, San Mateo, CA (1993).

[ARTICLES RELATED TO CHEMISTRY]

P. Tuffery and C. Etchebest and S. Hazout and R. Lavery, A New Approach
to the Rapid Determination of Protein Side Chain Conformations, Journal
of Biomolecular Structure & Dynamics, 8(6), 1267, (1991)

Thomas Dandekar and Patrick Argos, Potential of genetic algorithms in
protein folding and protein engineering simulations, Protein
Engineering 5(7), 637-645, (1992)

Denning, Peter J. Genetic algorithms, American Scientist, 80,
12-14, (1992).

E. Fontain, Application of Genetic Algorithms inthe Field of Constitutional
Similarity, J. Chem. Inf, Comput Sci, 32, 748-752, (1992)

John H. Holland, Genetic algorithms: computer programs that "evolve" in ways
that resemble natural selection can solve complex problems even their creators
do not fully understand, Scientific American 267, 66-72 [1992]

R.S.Judson, M.E. Colvin, J.C.Meza, A.Huffer, and D.Gutierrez.  Do
intelligent configuration search techniques outperform random search
for large molecules?  International Journal of Quantum Chemistry, 44,
277-290, (1992).

Richard S. Judson, Teaching Polymers to fold, The Journal of Physical
Chemistry, 96(25), 10102, (1992).

S. LeGrand and K. Merz, The application of the Genetic Algorithm to the
minimization of potential energy functions, J.Global Opt., (1992).

Wolfgang Linert, Peter Margl and Istvan Lukovits, Numerical Minimization
Procedures in molecular mechanics: structural modelling of the solvation of
beta-cyclodextrin, Computers & Chem. 16(1), 61-69, (1992).

Marcel J. J. Blommers, Carlos B. Lucasius, Gerrit Kateman and Robert
Kaptein, Conformational Analysis of a Dinucleotide Photodimer with the
Aid of the Genetic Algorithm, Biopolymers, Vol. 32, 45-52, (1992)

R.W. Smith, "Energy minimization in binary alloy models via genetic
algorithms" Comput.Phys.Comm. 71, 134-146, (1992).

Shaojian Sun, Reduced representation model of protein structure
prediction: Statistical potential and genetic algorithms, Protein
Science, 2, 762-785, (1993)

P. Tuffery, C. Etchebest, S. Hazout, and R. Lavery, A Critical Comparison of
Search Algorithms Applied to the Optimization of Protein Side-Chain
Conformations, J. Comp. Chem. 14, 790-798, (1993).

Ron Unger and John Moult, Genetic Algorithms for Protein Folding
Simulations, Journal of Molecular Biology, 231, 75-81, (1993).

R. Wehrens, C. Lucasius, L. Buydens, and G. Kateman, Sequential Assignment
of 2D-NMR Spectra of Proteins Using Genetic Algorithms, J. Chem. Info.
Comput. Sci.  33, 245-251 (1993).

Jones, Brown, Clark, Willett and Glen.  Searching Databases of Two-Dimensional
and Three-Dimensional Chemical Structures Using Genetic Algorithms, in Forest,
S. ed., Proceedings of the Fifth International Conference on Genetic 
Algorithms, Morgan Kaufmann Publishers, San Mateo, CA (1993).

R.S. Judson, E. Jaeger, A. Treasurywala, Conformation searching methods
for small molecules II: A Genetic algorithm approach, J.Comp.Chem.
(1993, in press).

D.B. McGarrah and R.S. Judson, An analysis of the genetic algorithm
method of molecular conformation determination, J.Comp.Chem.
(1993, in press).

Clark, Jones, Willett, Glen and Kenny, Pharmacophoric Pattern Matching
In Files Of Three-Dimensional Chemical Structures: Comparison Of
Conformational-Searching Algorithms For Flexible Searching, Presented
at the 3rd Int. conference on Chemical Structures, Journal of Chemical 
Information and Computer Sciences, (1993, in press).

Y.L. Xiao and D.E. Williams, Genetic algorithm: a new approach to the
prediction of the structure of molecular clusters, Chem. Phys. Let. 
(1993, in press)

Y.L. Xiao and D.E. Williams, GAME: Genetic algorithm for minimization of
energy, an interactive program for three-dimensional intermolecular 
interactions, Comput. & Chem, (submitted)