An interaction-motif-based scoring function for protein-ligand docking

BMC Bioinformatics

Table 4 Top 30 protein-ligand interaction network motifs ranked by motif significance grades, SG.

Rank	Ligand atom types	Protein atom types	Occurrence	Significance grade	Motif type
1	HAL, HAL	CRN, S3N, S3N	31	11.79	5 connections
2	C2N, ORA	NRE, S3N, S3N	1	11.69	5 connections
3	HAL, HAL	S3N, S3N, S3N	6	11.67	4 connections, 2+2
4	C2N, ORA	CRP, S3N, S3N	1	10.89	5 connections
5	NRA, NRA	CRN, CRN, NRE	1597	10.71	Fully connected
6	HAL, HAL	NRE, O3B, S3N	5	10.62	5 connections
7	CRN, ORA	CRN, CRN, CRN	374	10.57	Fully connected
8	C2N, ORA	S3N, S3N, NRE	1	10.55	4 connections, 2+2
9	CRN, NLC	CRN, CRN, CRN	2372	10.54	Fully connected
10	CRP, NRA	CRN, CRN, CRP	5236	10.49	Fully connected
11	C2N, ORA	NRE, S3N, NLB	1	10.40	5 connections
12	NRA, NRA	CRN, CRN, CRP	2572	10.40	Fully connected
13	CRP, NRA	CRN, CRP, CRP	1227	10.36	Fully connected
14	C2N, C2N	CRN, CRN, NRE	66	10.29	Fully connected
15	HAL, HAL	CRP, O3B, S3N	8	10.29	5 connections
16	HAL, NLC	CRN, S3N, S3N	25	10.28	4 connections, 3+1
17	NRA, NRA	CRN, NRE, NRE	125	10.28	Fully connected
18	NRA, NRA	CRN, CRP, NRE	259	10.22	Fully connected
19	HAL, HAL	S3N, CRN, S3N	27	10.20	4 connections, 3+1
20	CRN, NLC	CRN, CRN, CRP	450	10.20	Fully connected
21	HAL, HAL	CRN, O3B, S3N	2	10.17	Fully connected
22	CRN, CRN	CRN, CRN, CRN	37501	10.12	Fully connected
23	CRP, CRP	CRN, CRP, CRP	1676	10.05	Fully connected
24	HAL, HAL	S3N, NRE, S3N	2	10.03	4 connections, 2+2
25	HAL, NLA	S3N, S3N, NLC	2	10.01	5 connections
26	NRA, NRA	CRN, CRN, CRN	6605	10.01	Fully connected
27	HAL, NLC	CRN, S3N, NLB	50	10.00	4 connections, 2+2
28	HAL, HAL	CRN, S3N, S3N	14	9.86	4 connections, 2+2
29	HAL, HAL	CRN, CRN, CRN	68	9.86	Fully connected
30	HAL, NLC	CRN, S3N, NLC	50	9.82	4 connections, 2+2

The occurrences were counted in the 6,276 protein-ligand complex structures used to construct the networks (see Methods). See Fig. 3 for the different motif types.

ISSN: 1471-2105