QRNAS: software tool for refinement of nucleic acid structures

BMC Structural Biology

Table 2 Performance of QRNAS on RNA Puzzle #1 models in terms of model accuracy, as compared to RNAfitme and sander from the AMBER package

RNA-Puzzles #1 models	RMSD [Å]				INF_all				INF_nWC				Clashscore
RNA-Puzzles #1 models	starting	QRNAS	RNAfitme	sander	starting	QRNAS	RNAfitme	sander	starting	QRNAS	RNAfitme	sander	starting	QRNAS	RNAfitme	sander
1_bujnicki_1	5.70	5.63	5.60	5.63	0.825	0.778	0.522	0.787	0.750	0.750	0.866	0.750	0.00	0.00	0.00	0.00
1_bujnicki_2	6.13	5.98	5.93	5.97	0.776	0.774	0.496	0.736	0.289	0.671	0.500	0.289	61.25	1.40	18.91	60.88
1_bujnicki_3	5.28	5.24	5.22	5.23	0.796	0.761	0.483	0.750	0.707	0.408	0.866	0.707	48.21	2.10	10.81	48.32
1_bujnicki_4	4.94	4.87	4.84	4.84	0.703	0.654	0.357	0.652	0.250	0.378	0.354	0.250	69.06	0.70	14.86	70.22
1_bujnicki_5	5.11	4.91	4.95	5.01	0.701	0.664	0.376	0.656	0.378	0.333	0.378	0.378	66.30	2.10	23.65	68.12
1_chen_1	4.34	4.32	4.31	4.38	0.901	0.809	0.457	0.789	0.000	0.577	0.289	0.000	0.00	0.00	0.00	0.00
1_das_1	3.96	4.06	4.08	4.06	0.812	0.812	0.499	0.812	0.671	0.671	0.577	0.671	2.80	0.00	0.00	2.80
1_das_2	4.46	4.46	4.48	4.45	0.778	0.769	0.499	0.778	0.500	0.671	0.750	0.500	3.50	0.00	0.00	4.20
1_das_3	3.42	3.48	3.50	3.48	0.843	0.851	0.522	0.843	0.894	0.894	0.750	0.894	2.80	0.00	0.00	4.20
1_das_4	3.91	4.12	4.12	4.11	0.819	0.818	0.522	0.819	0.816	0.816	0.816	0.816	2.80	0.00	0.00	2.80
1_das_5	4.56	4.80	4.79	4.79	0.743	0.750	0.480	0.743	0.750	0.577	0.577	0.750	2.80	0.00	0.00	2.80
1_dokholyan_1	7.18	7.12	7.10	7.13	0.785	0.720	0.503	0.737	0.671	0.500	0.500	0.671	26.15	0.00	10.13	26.59
1_major_1	4.32	4.47	4.48	4.43	0.885	0.814	0.522	0.770	0.577	0.866	0.866	0.577	54.99	2.78	14.19	51.89
1_santalucia_1	5.75	5.46	5.41	5.43	0.864	0.776	0.510	0.755	0.577	0.577	0.577	0.577	25.07	0.00	8.78	21.71
average	4.93	4.92	4.92	4.92	0.802	0.768	0.482	0.759	0.559	0.621	0.619	0.559	26.12	0.65	7.24	26.04

ISSN: 1472-6807