Computational prediction of protein-protein complexes

BMC Research Notes

Table 3 Minimization energy (in kJ/mol) and buried surface area (in Å ² ) values and interacting residues within 4.5 Å of residues in another protein in three complexes returned by ClusPro

Complex	Minimization Energy (kJ/mol)	Buried Surface Area* (Å²)	Interacting Residues**	Interacting Residues**
Complex	Minimization Energy (kJ/mol)	Buried Surface Area* (Å²)	TNFR1	HP986
Complex 1	−22354.95	1194.3 (4867.7)	C104, S105, L106, L108, N109, T111, H113, L114, C116	R3, I7, L76
Complex 5	−22624.33	1218.7 (4792.9)	Same as above	D1, R3, K4, Y5, I7, G9, W10, E13, R32, L33, N34, M35, I36, L76
Complex 10	−22538.17	1193.7 (4826.6)	Same as above	L76

*The numbers represent BSA calculated using Chothia (1976) van der Waals radii set, while those in parentheses represent BSA as calculated using Richards (1977) van der Waals radii set using Surface Racer program.
**The interacting residues here have been calculated using DeepView to identify those residues in HP986 that are within 4.5 Å of same TNFR1 residues in the complexes. Only those residues which are also present in the list generated by Meta-PPISP and ODA tool are listed.

ISSN: 1756-0500