Supplementary Materials

Pulim, V., Bienkowska, J., Berger B., LTHREADER: PREDICTION OF LIGAND-RECEPTOR INTERACTIONS USING LOCALIZED THREADING. Pacific Symposium on Biocomputing 12:64-75 (2007).

Table S1: Datasets: Long-chain 4-helical bundle and TNF-like cytokine ligands and receptor

4-Helical Bundle Cytokines
Abbreviation	Name
Ligands
EPO	Erythropoietin
CSF3	Colony stimulating factor 3
GH	Growth hormone
IL6	Interleukin 6
LIF	Leukemia inhibitory factor
OSM	Oncostatin M
CNTF	Ciliary neurotrophic factor
IL23	Interleukin 23
IL12	Interleukin 12
LEP	Leptin
PRL	Prolactin
Receptors
EPOR	Erythropoietin receptor
CSF3R	Colony stimulating factor 3 receptor
GHR	Growth hormone receptor
GP130	GP130
IL12R	Interleukin 12 receptor
LEPR	Leptin receptor
PRLR	Prolactin receptor

TNF-Like Cytokines
Abbreviation	Name
Ligands
TNFSF1	Lymphotoxin alpha (LTA)
TNFSF2	Tumor necrosis factor (TNF)
TNFSF3	Lymphotoxin beta (LTB)
TNFSF4	OX40 antigen ligand (OX40L)
TNFSF5	CD40 antigen ligand (CD40L)
TNFSF6	Fas antigen ligand (FASL)
TNFSF10	TNF-related apoptosis inducing ligand (TRAIL)
TNFSF11	Receptor activator of NF-kappa-B ligand (RANKL)
TNFSF12	TNF-related weak inducer of apoptosis (TWEAK)
TNFSF13	APOL-related leukocyte expressed ligand 2 (APRIL)
TNFSF13B	B-cell activating factor (BAFF)
TNFSF15	TNF ligand-related molecule 1 (TL1A)
Receptors
TNFRSF1A	Tumor necrosis factor receptor 1 (TNFR1)
TNFRSF1B	Tumor necrosis factor receptor 2 (TNFR2)
TNFRSF4	OX40 antigen (OX40)
TNFRSF5	CD40 antigen (CD40)
TNFRSF6	Fas antigen (FAS)
TNFRSF6B	Decoy receptor 3 (DcR3)
TNFRSF10B	TNF-related apoptosis-inducing ligand receptor 2 (TRAILR2)
TNFRSF11A	Receptor activator of NF-kappaB (RANK)
TNFRSF11B	Osteoprotegerin (OPG)
TNFRSF12	DR3
TNFRSF12A	Type I transmembrane protein Fn14
TNFRSF13B	Transmembrane activator and CAML interactor (TACI)
TNFRSF13C	B-cell activating factor receptor (BAFFR)
TNFRSF17	B-cell maturation factor (BCMA)
LTBR	Lymphotoxin B receptor

Table S2: Datasets: Template complexes

4-Helical Bundle Cytokine Complexes
Ligand	Receptor	PDB ID
CSF3	CSF3R	1cd9
EPO	EPOR	1cn4
GH	GHR	1hwg
IL6	GP130	1p9m
LIF	GP130	1pvh

TNF-Like Cytokine Complexes
Ligand	Receptor	PDB ID
TNFSF10	TNFRSF10B	1dog
TNFSF13	TNFRSF13B	1xu1
TNFSF13	TNFRSF17	1xu2
TNFSF13B	TNFRSF13C	1oqe
TNFSF13B	TNFRSF17	1oqd

Table S3: Comparison of single and combined scoring methods using 1-fold cross validation on experimentally confirmed binding and non-binding pairs of ligands and receptors. “YES” indicates the method predicted the pair binds, “NO” that the pair does not bind. Green shading indicates that the prediction agrees with experimental data; red that it does not. See Section 3.3 for definitions of the CM, SP, FF and CR scoring methods. The significance of predicting interactions is equals to 1 minus the frequency of predicting interactions between pairs using randomized interaction surfaces.

4-Helical Bundle Cytokines
Ligand	Receptor	Binding?
Binding Pairs		Exp	CM	SP	FF	CR	All
EPO	EPOR	YES	NO	YES	YES	NO	YES
CSF3	CSF3R	YES	NO	YES	NO	YES	NO
GH	GHR	YES	YES	YES	NO	YES	YES
IL6	GP130	YES	YES	NO	NO	YES	YES
LIF	GP130	YES	NO	NO	YES	YES	YES
OSM	GP130	YES	YES	YES	NO	NO	YES
CNTF	GP130	YES	YES	YES	YES	YES	YES
CTF1	GP130	YES	YES	YES	NO	NO	YES
IL23	IL12R	YES	YES	YES	NO	YES	YES
IL12	IL12R	YES	YES	NO	NO	YES	YES
LEP	LEPR	YES	NO	NO	YES	NO	NO
PRL	PRLR	YES	NO	YES	NO	NO	NO
Non-Binding Pairs
IL6	EPOR	NO	NO	NO	NO	NO	NO
IL6	CSF3R	NO	YES	YES	NO	NO	YES
CSF3	EPOR	NO	NO	NO	NO	NO	NO
LEP	GHR	NO	NO	NO	NO	YES	NO
OSM	CSF3R	NO	NO	YES	NO	YES	NO
LEP	GP130	NO	NO	NO	NO	YES	NO
GH	GP130	NO	NO	YES	NO	YES	NO
EPO	GP130	NO	NO	YES	NO	NO	NO
IL12	GP130	NO	NO	YES	NO	NO	NO
IL23	GP130	NO	NO	YES	NO	NO	NO
IL12	EPOR	NO	NO	NO	NO	NO	NO
IL23	EPOR	NO	NO	NO	NO	NO	NO
IL6	PRLR	NO	NO	YES	NO	NO	YES
IL12	LEPR	NO	NO	NO	NO	YES	NO
Sensitivity			58%	67%	33%	50%	75%
Specificity			93%	50%	100%	64%	86%
Significance							0.62

TNF-Like Cytokines
Ligand	Receptor	Binding?
Binding Pairs		Exp	CM	SP	FF	CR	All
SF1	RSF1A	YES	NO	NO	NO	YES	YES
SF1	RSF1B	YES	NO	NO	NO	NO	YES
SF1	RSF14	YES	NO	NO	NO	YES	YES
SF2	RSF1A	YES	NO	NO	NO	YES	YES
SF2	RSF1B	YES	NO	NO	YES	NO	YES
SF3	RSF1A	YES	NO	YES	NO	NO	NO
SF3	RSF1B	YES	YES	YES	NO	YES	YES
SF3	LTBR	YES	YES	NO	NO	NO	YES
SF4	RSF4	YES	NO	NO	NO	YES	YES
SF5	RSF5	YES	NO	YES	NO	NO	NO
SF6	RSF6	YES	NO	NO	YES	YES	YES
SF6	RSF6B	YES	NO	NO	YES	YES	YES
SF10	RSF11B	YES	NO	NO	NO	NO	YES
SF11	RSF11A	YES	NO	YES	NO	NO	NO
SF11	RSF11B	YES	NO	YES	NO	NO	YES
SF12	RSF12A	YES	NO	NO	YES	YES	YES
SF13	RSF17	YES	NO	NO	NO	YES	NO
SF13B	RSF17	YES	NO	NO	NO	YES	NO
SF15	RSF6B	YES	NO	NO	YES	NO	NO
SF15	RSF12	YES	NO	YES	YES	YES	YES
Non-Binding Pairs
SF1	LTBR	NO	YES	YES	NO	NO	NO
SF1	RSF4	NO	YES	NO	NO	YES	YES
SF1	RSF5	NO	YES	YES	NO	NO	YES
SF2	RSF6	NO	NO	NO	NO	YES	NO
SF2	RSF6B	NO	YES	YES	NO	YES	YES
SF3	RSF11A	NO	YES	YES	NO	NO	NO
SF3	RSF11B	NO	NO	YES	NO	YES	NO
SF3	RSF12A	NO	NO	NO	NO	YES	NO
SF4	RSF17	NO	YES	NO	NO	YES	YES
SF5	RSF6B	NO	YES	NO	NO	NO	NO
SF6	RSF12	NO	NO	YES	NO	YES	YES
SF6	LTBR	NO	YES	YES	YES	NO	NO
SF10	RSF4	NO	YES	YES	NO	YES	NO
SF11	RSF5	NO	YES	YES	NO	NO	NO
SF11	RSF6	NO	YES	YES	YES	YES	YES
SF12	RSF6B	NO	NO	YES	YES	YES	YES
SF13	RSF11A	NO	NO	YES	YES	YES	NO
SF13B	RSF11B	NO	YES	YES	NO	YES	NO
SF15	RSF12A	NO	YES	NO	YES	YES	YES
SF15	RSF17	NO	NO	NO	YES	YES	YES
Sensitivity			10%	30%	30%	55%	70%
Specificity			35%	35%	70%	30%	55%
Significance							0.81

Table S4: Comparison of sensitivity and specificity values for raw versus normalized scores for both the standalone CM and combined methods.

	Raw	Normalized
CM Sensitivity	33%	58%
CM Specificity	57%	93%
Combined Sensitivity	33%	75%
Combined Specificity	50%	86%

Table S5:

Query Ligand-Receptor Pair	Template Complex	% similarity of query ligand to template ligand	% of interacting residue pairs correctly identified (RAPTOR)	% of interacting residues correctly identified (LTHREADER)
GH-GHR	IL6-GP130	23	33	53
GH-GHR	EPO-EPOR	15	30	55
GH-GHR	CSF3-CSF3R	20	31	63
EPO-EPOR	IL6-GP130	24	29	51
EPO-EPOR	GH-GHR	25	44	43
EPO-EPOR	CSF3-CSF3R	18	31	58
IL6-GP130	GH-GHR	22	28	52
IL6-GP130	EPO-EPOR	17	40	63
IL6-GP130	CSF3-CSF3R	21	42	66
CSF3-CSF3R	IL6-GP130	24	51	57
CSF3-CSF3R	EPO-EPOR	19	33	61
CSF3-CSF3R	GH-GHR	25	32	52
Average		21	35	56

Table S6:

Query Ligand-Receptor Pair	Template Complex	% similarity of query receptor to template receptor	% of interacting residue pairs correctly identified (RAPTOR)	% of interacting residues correctly identified (LTHREADER)
TNFSF13B-TNFRSF17	TNFSF13-TNFRSF13B	23	41	68
TNFSF13B-TNFRSF17	TNFSF10-TNFRSF10B	16	30	55
TNFSF13B-TNFRSF17	TNFSF13B-TNFRSF13C	39	60	82
TNFSF13B-TNFRSF13C	TNFSF13-TNFRSF13B	29	35	65
TNFSF13B-TNFRSF13C	TNFSF10-TNFRSF10B	18	25	45
TNFSF13B-TNFRSF13C	TNFSF13B-TNFRSF17	39	54	66
TNFSF10-TNFRSF10B	TNFSF13-TNFRSF13B	29	56	54
TNFSF10-TNFRSF10B	TNFSF13B-TNFRSF17	16	32	58
TNFSF10-TNFRSF10B	TNFSF13B-TNFRSF13C	18	42	38
TNFSF13-TNFRSF13B	TNFSF13B-TNFRSF17	23	56	74
TNFSF13-TNFRSF13B	TNFSF10-TNFRSF10B	29	40	62
TNFSF13-TNFRSF13B	TNFSF13B-TNFRSF13C	29	45	84
Average		25	43	63