StructKernel is a software that calculates similarity between residue microenvironments in protein structures. It uses structural, physicochemical, and evolutionary similarity between two microenvironments. Protein structure kernel can be used for statistical inference of functional amino acids in protein structures.
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Bioinformatics. 2010 Aug 15;26(16):1975-82. doi: 10.1093/bioinformatics/btq319. Epub 2010 Jun 15.
Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.
Xin F, Myers S, Li YF, Cooper DN, Mooney SD, Radivojac P.