Prediction of protein-protein binding site by using core interface residue and support vector machine

BMC Bioinformatics

Table 4 Contribution of each descriptor

Composition of feature vector	Core cut-off = 0.2	Core cut-off = 0.8
All descriptors	69.2%	84.8%
Without number of atom	0%	-0.1%
Without number of charge	-0.2%	-0.2%
Without number of H-bond	-0.1%	0%
Without hydrophobic index	-0.3%	-0.1%
Without relative accessible surface area	-0.6%	-0.8%
Without secondary structure	-0.2%	-0.3%
Without conservation score	-1.4%	-0.9%
Without side-chain environment	-0.4%	-0.5%
Without sequence distance	-0.1%	-0.1%
Without spatial distance	-0.2%	0%
Without residue composition	-0.4%	-0.1%
Without atom composition	-0.1%	-0.2%
Without total charge number	-0.1%	0%
Without total H-bond number	-0.1%	0%

This table shows the results of leave-one-out test for models built when the core cut-offs equal to 0.2 and 0.8 respectively. The first column is the composition of feature vectors. The second and the third columns are the CVA results of core cut-off = 0.2 and core cut-off = 0.8, respectively. The second line shows the CVA results of using all descriptors of both cut-offs. The values from the third line to the sixteenth line are the difference between the CVA of each leave-one-out test and the CVA using all descriptors.

ISSN: 1471-2105