. 2008 Sep;11(8):677–685. doi: 10.2174/138620708785739899

Table 1.

A Typology of Kernels for Proteins

Strategy	Input Data	Examples
Define a list of descriptors	Sequence	Physico-chemical kernels [46, 47] Spectrum, mismatch kernels [48-51] Pairwise motif kernel [52-54]
Define a list of descriptors	3D Structure	Kernel based on 3D descriptors [3]
Derive a kernel from a generative model	Sequence	Fisher, TOP kernels [1, 55] Mutual information kernels [56] Marginalized kernels [19, 57, 58]
Derive a kernel from a generative model	3D Structure	Random walk kernels [59]
Derive a kernel from a measure of similarity	Sequence	Local alignment kernel [22, 60-63]
Derive a kernel from a measure of similarity	3D Structure	Structure alignment kernel [25]