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    STUDIA CHEMIA - Issue no. 2 / 2008  
         
  Article:   GRID-BASED CONFORMATIONAL SAMPLING.

Authors:  BENJAMIN PARENT, ALEXANDRU TANTAR, NOUREDINE MELAB, EL-GHAZALI TALBI, DRAGOŞ HORVATH. 		 
       
         
  Abstract:  Computational simulations of conformational sampling in general, and of macromolecular folding in particular represent one of the most important and yet one of the most challenging applications of computer science in biology and medicinal chemistry. This paper presents a massively parallel GRID-based conformational sampling strategy, exploring the extremely rugged energy response surface in function of molecular geometry, in search of low energy zones through phase spaces of hundreds of degrees of freedom. We have generalized the classical island model deployment of Genetic Algorithms (GA) to a “planetary” model where each node of the GRID is assimilated to a “planet” harboring quasi-independent multi-island simulations using a hybrid GA.  
         
     
         
         
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