THREADER is a software of threading which is an approach to fold recognition which used a detailed 3-D representation of protein structure. The idea was to physically “thread” a sequence of amino acid side chains onto a backbone structure (a fold) and to evaluate this proposed 3-D structure using a set of pair potentials and (importantly) a separate solvation potential.
Bioinformatics Group – University College London
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Jones, D.T., Miller, R.T. & Thornton, J.M. (1995)
Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing.
Proteins. 23, 387-397.