Genetic algorithms representation

S. Sun, Reduced representation model of protein structure prediction statistical potential and genetic algorithms. Protein Sci. 2 (1993), 762-785. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

Abraham, N.L. and Probert, N.J., A periodic genetic algorithm with real space representation for crystal structure and polymorph prediction, Phys. Rev. B., 73, 224106,2006. 

Fig. 5. Representation of a genetic algorithm for the selection of descriptors for a QSAR model. The model is commonly referred to as a gene and is encoded with different descriptors. Two Parents creating two Children is a crossover of genetic information (descriptors). The genes of an individual can mutate, introducing random changes in the model. Crossover and mutation are can occur independent of each other.

Two aspects of the system must be modeled in order to use the idea of genetic algorithms for an application like molecular docking. First, a linear representation of a configuration such as a bit string is needed describing all... 

The main focus of this article is the application of genetic algorithm (GA) techniques to solve crystal structures of molecular materials directly from powder diffraction data (Sect. 2). In this application, the aim is to find the set of atomic positions (x,y, z) [knowing the unit cell a, b, c, a, y and space group S] that give the optimal representation of an experimental powder diffraction pattern. In such applications, the population in the evolutionary algorithm com-... 

Figure 5 A schematic representation of the way children structures are created from the parent structures in the genetic algorithms when using a one parent -> one child strategy. The parent in the left panel is cut into two halves (made clear through the different symbols for the two different parts as well as through the dashed line that marks the cut) that subsequently are interchanged leading to the structure of the right panel...

Chromosome in a genetic algorithm is a representation for data and solutions consisting of real numbers or bit values that represent the presence or absence of features. 

PROTEIN-PROTEIN DOCKING USING THREE-DIMENSIONAL REDUCED REPRESENTATIONS AND BASED ON A GENETIC ALGORITHM... 

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