Reconfigurable hardware computing for accelerating protein folding simulations using the harmony search algorithm and the 3D-HP-side chain model

Abstract

Proteins are essentials to life and they have countless biological functions. They are synthesized in the ribosome of cells following a template given by the messenger RNA (mRNA). During the synthesis, the protein folds into an unique three-dimensional structure, known as native conformation. This process is called protein folding. Several diseases are believed to be result of the accumulation of ill-formed proteins.Therefore, understanding the folding process can lead to important medical advancements and development of new drugs. © 2011 Springer-Verlag.