Genetic algorithms conformational analysis

Other methods which are applied to conformational analysis and to generating multiple conformations and which can be regarded as random or stochastic techniques, since they explore the conformational space in a non-deterministic fashion, arc genetic algorithms (GA) [137, 1381 simulation methods, such as molecular dynamics (MD) and Monte Carlo (MC) simulations 1139], as well as simulated annealing [140], All of those approaches and their application to generate ensembles of conformations arc discussed in Chapter II, Section 7.2 in the Handbook. 

A molecular dynamics simulation samples the phase space of a molecule (defined by the position of the atoms and their velocities) by integrating Newton s equations of motion. Because MD accounts for thermal motion, the molecules simulated may possess enough thermal energy to overcome potential barriers, which makes the technique suitable in principle for conformational analysis of especially large molecules. In the case of small molecules, other techniques such as systematic, random. Genetic Algorithm-based, or Monte Carlo searches may be better suited for effectively sampling conformational space. 

Lucasius CB, Blommers MJJ, Buydens LMC, Kateman G (1991) A genetic algotithm for conformational analysis of DNA. In Davis L (ed) Handbook of genetic algorithms. Van Nostrand Reinhold, New York... 

Methods of Quantum Pharmacology for Conformational Analysis Monte Carlo Methods, Molecular Dynamics, Genetic Algorithms... 

McGarrah, D. B., Judson, R. S. Analysis of the genetic algorithm method of molecular conformation determination. J. Comput. Chem. 1993,14,1385-1395. 

In general, five different approaches can be distinguished and are applied to explore the conformational space of a molecule systematic searches, rule-based and data-based approaches (model building), random methods, genetic algorithms, distance geometry, and simulation methods. Some of the basic principles and ideas behind these concepts have already been described in the Secs. 2 and 3 of this article. In the following, the application of these concepts to conformational analysis and searches will be discussed. 

McGarrah D B and R S Judson 1993. Analysis of the Genetic Algorithm Method of Molecular-conformation Determination. Journal of Computational Chemistry 14 1385-1395... 

D. B. McGarrah and R. S. Judson,/. Comput. Chem., 14, 1385 (1993). An Analysis of the Genetic Algorithm Method of Molecular Conformation Determination. 

AutoDock provides several methods for doing the conformation search however, the Lamarckian Genetic Algorithm (LGA) [41] provides the most efficient search for general applications and was our choice for the docking analysis. LGA begins with a population of random substrate conformations in random orientations and we... 

One of the problems with the loose definition of AI is that it is often difficult to determine if a program is an example of AI in chemistry. As mentioned above, neural nets are no longer considered to be AI and so will not be covered here. The use of genetic algorithms is another area that has been used to perform conformational analysis, but which is no longer considered to be core AT. Both of these subjects are covered in their own separate articles in this encyclopedia. 

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