Threading Onion Model

In a nutshell there are two families of energy functions that are used in threading computations, namely the pairwise models (with identifiable pair interactions) and the profile models. In this section we formally define both families and we also introduce a novel THreading Onion Model (THOM), which is investigated in the subsequent sections of the chapter. 

We consider two profile models. The first, which is very simple, was used in the past as an effective solvation potential [1,2,42], We call it THOMl (THread-ing Onion Model 1), and it suggests a clear path to an extension (which is our prime model), namely, THOM2. The onion level denotes the number of contact shells used to describe the environment of the amino acid. The THOMl model uses one contact shell of amino acids. The more detailed THOM2 energy model (to be discussed below) is based on two layers of contacts. 

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