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Structural classification shows that the number of different protein folds issurprisingly small. It also appears that proteins are built in a modularfashion, from a relatively small number of components. Here we propose toidentify the modular building blocks of proteins with the dark soliton solutionof a generalized discrete nonlinear Schrodinger equation. For this we show thatpractically all protein loops can be obtained simply by scaling the size and byjoining together a number of copies of the soliton, one after another. Thesoliton has only two loop specific parameters and we identify their possiblevalues in Protein Data Bank. We show that with a collection of 200 sets ofparameters, each determining a soliton profile that describes a different shortloop, we cover over 90% of all proteins with experimental accuracy. We alsopresent two examples that describe how the loop library can be employed both tomodel and to analyze the structure of folded proteins.

Soliton concepts and the protein structure