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Folding proteins with a Transgenic Algorithm
Throughout the history of science, mother nature has always been a rich source of inspiration. Four billion years of a painful trial- and error process known as
"evolution" provide an inexhaustible reservoir of elegant answers to a variety of difficult questions. During the development of YASARA's fold prediction module
YASARA FOLD, we took a close look at the current state of life and concluded that since the first mating of eukaryotic cells
(which forms the basis of the now widely used genetic algorithms), a quantum-leap occurred,
that has not yet found its counterpart in fold prediction: Due to the advent of genetic engineering,
the phenotype has in principle gained access to its genotype, with genome sequencing,
annotation and gene therapy providing a directed feedback-loop, that heavily exceeds the possibilities of random Darwinian evolution.
YASARA FOLD has therefore been based on a transgenic algorithm that mimics nature's latest evolutionary achievement: genetic engineering. The genotypes are sets of inter-atomic distances, and the phenotypes are the corresponding three-dimensional coordinates. In addition to the usual steps takes by genetic optimization algorithms (mutation, crossover and selection), YASARA can build and modify genotypes in a rational manner, correct "bad" genes, choose "good" ones for mating or propagate "useful" abilities acquired during lifetime (i.e. molecular dynamics simulations) back to the genome (using a process called impression or reverse expression, bringing Lamarck's ideas back to life).
Click here for a more detailed description of the 10 steps to Transgenic Fold Prediction.