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Title: DSGA and GA from 'Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding '

Type Software Brown, Michael, Bennett, Tommy, Coker, James A. (2014): DSGA and GA from 'Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding '. Zenodo. Software. https://zenodo.org/record/11902

Authors: Brown, Michael (University of Maryland) ; Bennett, Tommy (University of Maryland) ; Coker, James A. (University of Maryland) ;

Links

Summary

Dynamic-radius Species-conserving Genetic Algorithm for de novo Protein Folding Instructions

Dynamic-radius Species-conserving Genetic Algorithm for de novo Protein Folding is a Java application written in Java version 1.7, but it should run on other versions of Java.

There are 10 command line parameters that should be set:

# position 1 - population size # position 2 - number of generations # position 3 - mutation rate (decimal) # position 4 - initial radius (decimal) # position 5 - radius delta (decimal) # position 6 - reevaluation loop count # position 7 - convergence limit # position 8 - protein # position 9 - output file location # position 10 - log status 0 few logs; 1 more logs; 2 most logs

An output file will be placed in the file location for position 9. 

Here is an example for running the application:

java -jar /Users/mbrown15/NetBeansProjects/DSGAProteinFolding/dist/DSGAProteinFoldingKG.jar 1000 2000 0.03 8.0 -1.0 500 4 PPHPPHHPPHHPPPPPHHHHHHHHHHPPPPPPHHPPHHPPHPPHHHHH //Users//mbrown15//Documents//genetic-algorithm-files// 1

 

This method allows multiple runs to be placed in a batch file. 

The class called TestAllCombinationsSample will generate a file for Figure 2. 

The file GAProteinFoldingDD has the code for the traditional Genetic Algorithm.

More information

  • DOI: 10.5281/zenodo.11902

Subjects

  • genetic algorithm, dynamic species-conserving genetic algorithm, DSGA, protein folding

Dates

  • Publication date: 2014
  • Issued: September 29, 2014

Rights

Much of the data past this point we don't have good examples of yet. Please share in #rdi slack if you have good examples for anything that appears below. Thanks!

Format

electronic resource

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