Flow chart of our SVM-based methods. The structure-based method (SVM-3D) takes in input mutation (yellow) structure environment (in blue), sequence profile (green), PANTHER output (pink) and function (gray) information. In the sequence-based method (SVM-SEQ) the 21 elements vector encoding for the structural environment is replaced by the 20 elements vector encoding for the sequence environment. The structure environment is the residue composition in a 6 Å radius shell around the C-a of the mutated residue. The sequence environment is the amino acid composition window of 19 residues centred on the mutated residue.
Capriotti and Altman BMC Bioinformatics 2011 12(Suppl 4):S3 doi:10.1186/1471-2105-12-S4-S3