Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins

BMC Bioinformatics

Table 2 Performance tests on an Intel i7-8565U CPU: RINmaker versus RING 3.0 versus PDBe-Arpeggio

PDB name	Num. of residues	CPU time (s) with hydrogen addition			CPU time (s) without hydrogen addition
PDB name	Num. of residues	RINmaker	RING 3.0	PDBe-Arpeggio	RINmaker	RING 3.0
1al1	12	0.0885	0.948	1.22	0.005	0.961
1l2y	20	0.0987	0.996	1.51	0.005	0.963
1bk8	50	0.0934	0.991	8.17	0.004	0.989
1eod	100	0.0975	1.031	6.64	0.009	0.994
1hhq	150	0.108	1.077	15.26	0.009	1.017
1ab5	250	0.115	1.118	63.25	0.015	1.036
1bge	318	0.120	1.209	131.50	0.022	1.119
1b1y	500	0.147	1.539	185.03	0.037	1.292
2vji	598	0.167	1.672	436.09	0.049	1.340
1miq	750	0.183	1.752	447.50	0.050	1.410
1a3w	1000	0.241	1.888	789.72	0.061	1.661
6j8j	1433	0.350	2.793	2245.17	0.084	2.210
1h1l	1994	0.604	3.417	7771.14	0.150	2.905
1i84	2382	0.506	3.594	\(>8000.00\)	0.143	2.923
3dwk	2444	0.619	4.067	\(>8000.00\)	0.185	3.416
3aae	2758	0.715	3.929	\(>8000.00\)	0.184	3.510
2qmi	3573	1.047	6.075	\(>8000.00\)	0.269	5.316
7fd2	4060	1.35	6.640	\(>8000.00\)	0.259	5.717

ISSN: 1471-2105