Proteins form the very basis of life. If we were to open up any living cell, we would find, apart from DNA and RNA molecules whose primary role is to store genetic information, a large number of different proteins that comprise the cell itself (for example the cell membrane and organelles), as well as a diverse set of enzymes that catalyze various metabolic reactions. If enzymes were absent, the cell would not be able to function, since a number of metabolic reactions would not be possible. Functions of proteins are the consequences of their functional 3D shape. Therefore, to control these versatile properties, we need to be able to predict the 3D shape of proteins; in other words, solve the protein folding problem. The prediction of a protein’s conformation from its amino-acid sequence is currently one of the most prominent problems in molecular biology, biochemistry and bioinformatics. In this thesis, we address the protein folding problem and the closely-related problem of identifying folding pathways. The leading research objective for this work was to design efficient heuristic search algorithms for these problems, to empiricall
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