Subject: Re: GA and Protein Folding?

From: [email-masked] (Mark Dalton)
Date: Wed, 11 May 1994 14:22:21 -0500 (CDT)

This is from the News group comp.ai.genetic.
One ftp/mosaic site to check is: alife.santafe.edu or sfi.santafe.edu.

<HR>
<H2>Reasoning, Systems theory, Chaos and Artificial Intellegence</H2> 
<UL>
<LI><A HREF="http://pespmc1.vub.ac.be/CYBSYSTH.html"><B>Cybernetics and Systems Theory</B></A>
<LI><A HREF="http://mosaic.reasoning.com/home.html"><B>Reasoning Systems Home Page</B></A>
<LI><A HREF="http://pespmc1.vub.ac.be/"><B>Welcome to the Principia Cybernetica Web</B></A>
<LI><A HREF="http://wwwhost.cc.utexas.edu/cc/staff/mccoy/gp/gp.html"><B>Genetic Programming</B></A>
<LI><A HREF="http://medg.lcs.mit.edu/"><B>Clinical Decision Making Group</B></A>
<LI><A HREF="http://www.ai.mit.edu/"><B>MIT AI lab Web home page</B></A>
<LI><A HREF="http://ai.iit.nrc.ca/home_page.html"><B>Knowledge Systems Laboratory - Home Page</B></A>
<LI><A HREF="http://www.seas.upenn.edu/~ale/cplxsys.html"><B>Complex (Adaptive) Systems Information</B></A>.
<LI><A HREF="http://life.anu.edu.au/complex_systems/complex.html"><B>Complex sytems in Australia</B></A> - Good list of programming models links.
<LI><A HREF="http://www.msrc.pnl.gov:2080/docs/cie/neural/neural.homepage.html"><B>Neural Networks</B></A> - a very good NN page.
<LI><A HREF="http://cnls-www.lanl.gov/"><B>Center for Nonlinear Studies</B></A>
<LI><A HREF="http://mosaic.reasoning.com/home.html"><B>Reasoning Systems' QA & engineering Tools</B></A>.
</UL>
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Subject: (fwd) Re: Genetic algorithms for Protein Folding - Request
Newsgroups: comp.ai.genetic
Status: RO

Subject: Re: Genetic algorithms for Protein Folding - Request
Date: 06 Apr 94 20:50:48 GMT
Organization: Supercomputer Computations Research Institute
Message-ID: <[email-masked]>
References: <[email-masked]>
NNTP-Posting-Host: ibm1.scri.fsu.edu
In-reply-to: [email-masked]'s message of 06 Apr 94 13:27:31 EST

In article <[email-masked]> [email-masked] (Alan Bryant Heirich) writes:
 > Has anyone used genetic algorithms to solve the protein
 > folding problem for DNA?
 >
 > I'm interested in any published material -- thanks in advance.

Here's a list of references, compiled by Melanie Mitchell,
that I found very useful.

From: [email-masked] (Melanie Mitchell)
To: [email-masked], [email-masked]
Subject: GAs and protein folding bibliography
Date: Thu, 18 Nov 93 11:01:14 MST

Thanks to all who responded to my query about GAs and protein folding.  Here is
a compiled list of citations I was sent on GAs and various aspects of protein
folding and related areas.  

Many people expressed interest in this list, so if anyone has any additional
citations to add, please post them to the list.  

Melanie Mitchell

------------------------------

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)

Bouzida,D.,S.Jumar, and R.H.Swendsen, "A Simulated Aneeling Appproach
for Probing Biomolecular Structures", 26th Hawaii International Conference on 
System Sciences, vol.I, IEEE, 1993

Cedeno, Walter.  DNA restriction fragment map assembly with genetic
algorithms.  In Genetic Algorithms at Stanford 1993.  Stanford, CA:
Stanford University Bookstore. 1993.

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).

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

David Eisenberg, Determining Protein Folds by Inverted and
Evolutionary Protein Folding Algorithms", Proceedings of the North
Caroline Symposium on Molecular Modeling: Integration of Theory and
Experiment, Research Triangle Park, North Carolina,21-23, 1993.

Fickett, James W. and Cinkosky, Michael J.  A genetic algorithm for
assembling chromosome physical 
maps.  Unpublished draft 1993.

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

M. S. Freidrichs and P. G. Wolynes, Genetic algorithms for model biomolecular
optimization problems.  Unpublished manuscript.  Noyes Lab., University of
Illinois, Urbana, Il, 61801. 

S. Handley, Automated learning of a detector for helices in protein
sequences via genetic programming.  In 
S. Forrest (Ed.), Proceedings of the Fifth International Conference
on Genetic Algorithms. Morgan Kaufmann, San Mateo, CA. 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).

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

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

Akihiko Konagaya, A stochastic approach to genetic information
processing.  Institute for New Generation Computer Technology, ICOT
Technical Memorandom: TM-1263", May, 1993.

Konagaya,A. and H.Kondo,"Stochastic Motif Extraction using a Genetic
Algorithm with the MDL principle"., 26th Hawaii International Conference on 
System Sciences, vol.I, IEEE, 1993

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

Leopold,P.E. and E.I.Shakhnovich, "Protein Folding Kinetics in the
Dense Phase", 26th Hawaii International Conference on System Sciences, 
vol.I, IEEE, 1993

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).

C. B. Lucasius and G. Kateman, Application of genetic algorithms in 
chemometrics.  In J. D. Schaffer (Ed.), Proceedings of the third international
conference on genetic algorithms.  Morgan Kaufmann, San Mateo, CA. 1989. 

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

Platt,D.M. and T.I.Dix,"Construction of Restriction Maps Using a
Genetic Algorithm", 26th Hawaii International Conference on 
System Sciences, vol.I, IEEE, 1993

S. Schulze-Kremer, Genetische Algorithmen zur Vorhersage von
Proteintertiaerstrukturen, in Fortschritte der Simulation in Medizin,
Biologie und Oekologie, (D.P.F. Moeller, O. Richter Hrsg.), Technische
Universitaet Clausthal- Zellerfeld, Institut fuer Informatik, pp. 
217-238, 1992.
 
Steffen Schulze-Kremer, Genetic Algorithms in Biochemistry (GALB):
Learning Protein Folding Pathways.  In Joachim Stender (Ed.), Parallel
Genetic Algorithms.  IOS Press, Amsterdam. 1992.

S. Schulze-Kremer, Genetic algorithms for protein tertiary structure
prediction.  In R. Manner and B. Manderick (Eds.), 
Parallel Problem Solving from Nature 2, pp. 391-400. 
North Holland, Amsterdam, 1992.  

S. Schulze-Kremer, U. Tiedemann, Genetic Algorithms for Protein
Tertiary Structure Prediction, in Artificial Intelligence and Genome
Workshop 26, (J.-G. Ganascia Ed.), International Joint Conference on
Artificial Intelligence, Institut Blaise Pascal, Paris, pp. 119-141,
1993.

S. Schulze-Kremer, U. Tiedemann, Parameterizing Genetic Algorithms
for Protein Folding Simulation, to appear in the Proceedings of the 27th 
Hawaii International Conference on System Sciences, 1994. 

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)

Joachim Stender and Tom Addis, Using the Genetic Algorithm to Adapt
Intelligent Systems.  In Symbols versus Neurons?.  IOS Press,
Amsterdam, 1990.

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)

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).

R. Unger and J. Moult,
A genetic algorithm for 3D Protein Folding Simulations,
In S. Forrest (Ed.), 
Proceedings of the Fifth International Conference on Genetic Algorithms,
581-588. Morgan Kaufmann, San Mateo, CA. 1993. 

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

Unger,R. and J. Moult, "On the applicability of genetic algorithms to
protein folding", 26th Hawaii International Conference on System Sciences, 
vol.I, IEEE, 1993

Jukka Vanhala and Kimmo Kaski, Protein folding simulation by genetic
algorithms.  In Risto Nieminen and Olle Teleman (Eds.), 7th Nordic
Symposium on Computer Simulation, Espoo, Finland, 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).

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)

D. C. Youvan and A. P. Arkin and M. M. Yang, Recursive ensemble
mutagenesis - A combinatorial optimization technique for protein
engineering.  In R. Manner and B. Manderick (Eds.), Parallel Problem
Solving from Nature 2.  North Holland, Amsterdam, 1992.

--
Kingsley F. Kerce ([email-masked])    WWW: http://www.scri.fsu.edu/~kerce
Supercomputer Computations Research Institute
Florida State University
Tallahassee, FL, USA  32306	 DEEP THOUGHT: I'd rather be rich than stupid.

-- 
Mark Dalton                   AUG-GCU-AGA-AAG                  H      
Cray Research, Inc.           M   A   R   K                    |     
Eagan, MN 55121                                  CH3-S-CH2-CH2-C-COOH
Internet: [email-masked]                                         |   
(612)683-3035                                                  NH2

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Thoughts to ponder:
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Most difficult tasks are easy, it just depends on if you know the solution.
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