Table 2. Active site residues proposed for guided docking by HADDOCK. The structurally similar RNA-bound complexes used to identify interacting residues are given. If a related fold information was not used, ab-initio RNA prediction method used to predict binding sites, are listed. The residues proposed either based on structurally similar interactions or by ab-initio predictions, are listed in parentheses. Those added additionally to the list based on the vicinity to IRES RNA, are listed outside parentheses.

Ribosomal protein	Interface residues involved in docking restraints	Structurally similar interaction / Prediction	IRES bases
S5e	(V134,R136,R127), (T104,I178,K182,N186,Y188,K191,E195,R198,S202)	2WDM-G, 2NOQ-F	80–87, 67–73, 90–95, 97–101
S25	K114,(K66,R76)	Muhs et al. 2011	80–87, 67–73, 90–95, 97–101
S26	(R51,K66),Y62	BindN	305–308,329
S3a (S1e)	(K199, Q202)	RNABindR	299,300
S27	(K36,Y41,R80,Q83)	3IZR-m	234–237