ProSAT toolkit is a set of programs that allow building SVM based models for annotating amino acid residues in protein sequences using user supplied features (like PSI-BLAST profiles, or PSIPred profiles). In particular, the toolkit builds features using a window around the residue, and is equipped with a specialized kernel function (normalized second order exponential kernel function nsoe ) along with the standard svm kernel function.
Professsor Huzefa Rangwala (firstname.lastname@example.org) and Professsor George Karypis
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“A kernel framework for protein residue annotation“.
Huzefa Rangwala, Christopher Kauffman and George Karypis.
Lecture Notes in Computer Science Volume 5476, 2009, pp 439-451