Protein-protein docking using region-based 3D Zernike descriptors

BMC Bioinformatics

Table 2 Comparison of the combination of the scoring terms.

Complex	LZerD	3DZD+NORMAL	NORMAL	BSA	EXVOL	EXVOL +BSA
1A0O	704	11917	5320	848	5888	573
1AVW	41	26	31	958	7412	696
1AVZ	21	920	554	2237	332	77
1BQL	507	6604	294	10042	23281	935
1BRC	132	221	8657	4140	2335	1456
1BRS	1	3	1	20	14154	6
1BTH	1	1	1	18	10176	1
1CHO	1	1	1	534	98	97
1CSE	5	22	18	208	16286	182
1EO8	3791	7869	6472	12640	204	687
1FBI	202	4055	4004	7480	9164	1053
1FSS	26	4292	3904	204	4220	85
1GLA	1161	42275	39867	12647	1377	4074
1IAI	11	45	78	895	17448	25
1IGC	2946	5887	7988	6832	2292	1827
1JHL	2901	850	1413	8706	2191	1601
1MEL	125	30081	21657	533	3405	26
1QFU	17	54	57	2571	6279	115
1SPB	1	63	36	107	27227	4
1STF	2	13	8	101	2491	3
1TAB	20	31	40	271	2878	17
1TGS	1	1	1	426	837	11
1UGH	1	4	1	5	12311	1
2KAI	37	150	337	1750	775	374
2PTC	9	9	22	1781	12777	72
2TEC	2	536	514	9261	289	7184
2VIR	5243	18668	15018	3750	5063	9594
3HHR	351	16048	901	1332	8496	382
4HTC	1	1	1	1	17361	1
Summary
Wins vs. LZerD ^a)	-	3D+N/LZD 2/22	Normal/LZD 3/20	BSA/LZD 1/27	ExVol/LZD 4/25	E+B/LZD 6/20
Wins Overall ^b)	20	7	7	2	1	7

The training set included 29 bound-bound protein complexes taken from Benchmark datasets 0.0 and 1.0. The Rank and the iRMSD shown correspond to the best ranked hit with an interface RMSD ≤ 2.5 Å. The parameters for combining terms for the LZerD score and BSA + EXVOL are shown in Table 5. The abbreviations used are: BSA, the buried surface area term; EXVOL, the amount of clashes measured by the excluded volume; 3D+N, 3DZD+Normal; LZD, LZerD; E+B, EXVOL+BSA.
a) The number at "Wins vs LZerD" indicates the number of cases the either the ranking scheme or the LZerD shows a better rank than the other among the two scoring schemes. Ties are not counted.
b) The number at "Wins Overall" indicates the number of cases the ranking scheme reports the best rank. Wins are shown in bold in the table.

ISSN: 1471-2105