Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family

Table 4 Performance of the various functional site prediction schemes across all functional sites.¹

Method	Binding sites	Cytoplasmic gate	Extracellular gate
(a.) Unique methods
Phylogenetic motif	0.68; 0.18; 0.38	0.00; 0.00; 0.00	1.00; 0.06; 0.33
False positive expectation	0.63; 0.29; 0.43	0.00; 0.00; 0.00	0.60; 0.06; 0.28
Site conservation	0.46; 0.19; 0.31	1.00; 0.09; 0.93	0.80; 0.07; 0.33
Rate4Site	0.54; 0.28 0.39	0.20; 0.02; 0.10	0.60; 0.07; 0.28
ET	0.38; 0.16; 0.26	0.60; 0.05; 0.27	0.60; 0.05; 0.27
SDPpred	0.21; 0.56; 0.36	0.00; 0.00; 0.00	0.00; 0.00; 0.00
(b.) Hybrid methods
Union (PM + FPE)	0.88; 0.18; 0.41	0.00; 0.00; 0.00	1.00; 0.04; 0.32
Intersect_2	0.71; 0.20; 0.40	0.60; 0.04; 0.26	0.80; 0.05; 0.31
Intersect_3	0.42; 0.35; 0.38	0.20; 0.02; 0.10	0.60; 0.07; 0.28
Intersect_4	0.33; 0.36; 0.34	0.00; 0.00; 0.00	0.60; 0.14; 0.33
Intersect_5	0.13; 0.33; 0.22	0.00; 0.00; 0.00	0.60; 0.33; 0.45

¹ Each cell of the table includes: coverage; accuracy; and overall performance of the method on each subset of the complete benchmark dataset. The three subsets are defined in Table 2.

ISSN: 1471-2105