A protocol for CABS-dock protein–peptide docking driven by side-chain contact information

Table 1 Comparison of CABS-dock docking performance without (default) vs. with information about a randomly selected contact

	Docking without contact information (default CABS-dock settings)				Docking driven by random contact information
PDB	RMSD^10k	RMSD^1k	RMSD¹⁰⁰	RMSD¹⁰	RMSD^10k	RMSD^1k	RMSD¹⁰⁰	RMSD¹⁰
2v3s	2.42	2.42	3.48	8.89	1.30	1.37	1.65	1.77
2vj0	2.09	2.96	4.12	3.91	2.71	3.00	3.00	3.40
2zjd	2.35	2.69	2.79	4.60	1.77	2.03	2.03	3.06
3bfq	10.20	11.53	14.22	13.48	1.47	1.47	2.34	2.89
3bu3	6.87	7.06	7.71	8.86	3.62	4.45	5.33	5.47
3bwa	2.42	2.75	3.17	3.94	2.00	2.32	2.36	3.55
3cvp	4.52	4.67	8.47	10.14	2.37	2.98	3.91	4.29
3d1e	4.39	6.59	8.18	18.82	1.76	1.76	2.01	1.76
3d9t	3.56	4.34	7.25	10.06	1.96	2.69	3.42	3.72

The table shows RMSD values showing the lowest RMSD value from: 10,000 CABS-dock models (RMSD^10k), 1000 top-scored CABS-dock models (RMSD^1k), 100 top-scored CABS-dock models (RMSD¹⁰⁰), 10 top-scored CABS-dock models (RMSD¹⁰)

ISSN: 1475-925X