An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data

Table 1 Summary of results from the three analyses for the previously-investigated target PPIs

PPI	interacting Pfam domain	presence of pockets	GO
			S _i ^C	S _i ^F	S _i ^P
AMAP1/cortactin	PF00018/PF00018	-/no	8	6	0
B7.1/CD28	not identified	yes/yes	1	6	1
BAK/BCL2(BCL-X_L)	PF00452/PF02180, PF00452/PF00452	yes/yes	187**	19* (10)	396 (372)
β-catenin/Tcf4	PF00514/PF08347	yes/-	98*	23*	171**
CCR5/Env	not identified	-/no	60	1	8
CD4/MHC class II	PF00047/PF00993, PF00047/PF07654	yes/-	178**	30**	16
CRM1/Rev	not identified	yes/-	98*	10	115**
EPO/EPOR	PF00758/PF09067, PF00758/PF00041	yes/yes	1	6	10
IL1α (IL1β)/IL1R type I	PF00340/PF00047	yes/yes	8	11*	35**
IL2/IL2Rα	PF00715/PF00084	no/yes	1	6	88*
iNOS/iNOS	PF02898/PF02898, PF00258/PF00258, PF00258/PF00175, PF00258/PF00667, PF00667/PF00667, PF00667/PF00258, PF00667/PF00175, PF00175/PF00667, PF00175/PF00258, PF00175/PF00175	yes/yes	90*	122**	104**
LFA1/ICAM1	PF00092/PF03921	yes/yes	123**	15*	8
Myc/Max	PF00010/PF00010, PF02344/PF00010	no/no	98*	23*	133**
NGF/p75^NTR	PF00243/PF00020	yes/no	0	11*	93**
p53/MDM2	PF08563/PF02201	-/yes	362**	36**	233**

In the column of 'interacting Pfam domain', interacting partner domains identified by iPfam are shown. 'Domain a/domain b' in a row of a PPI shown by 'protein A/protein B' indicates that domain a in protein A and domain b in protein B interact with each other. In the column of 'presence of pockets', 'yes' means that one or more pockets were found by at least one of the two programs, 'no' means that no pocket was found, and '-' indicates that pockets were not searched because of lack of nearly identical tertiary structures. Statistical significance of similarity scores (S_i^C, S_i^F, and S_i^P) for GO-term assignment are indicated by '*' (* P < 0.05, ** P < 0.01). In the row of 'BAK/BCL2(BCL-X_L)', similarity scores for BAK/BCL-X_L are shown in parentheses.