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

BMC Bioinformatics

Table 1 Correlation coefficient of 3DZD for bound and unbound interfaces for some protein complexes from the ZDOCK Benchmark datasets.

PDB^a)	Class^b)	Difficulty^c)	#Atoms (R, L)^d)	ΔASA (Å²)^e)	3DZD Correlation for Bound interface	3DZD Correlation for Unbound interface
1AY7(1RGH;1A19)	E	E	747,721	1237	0.93	0.93
1CGI(2CGA;1HPT)	E	E	1800,441	2053	0.96	0.97
2PCC(1CCP;1YCC)	E	E	2339,847	1141	0.99	0.98
2SNI(1UBN;2CI2)	E	E	1932,521	1628	0.97	0.95
1ACB(2CGA;1EGL)	E	MD	1799,575	1544	0.94	0.95
1AHW(1FGN;1TFH)	A	E	3304,1622	1899	0.99	0.98
1FSK(1FSK;1BV1)	A	E	3347,1231	1623	0.95	0.89
1MLC(1MLB;3LZT)	A	E	3290,1000	1392	0.97	0.96
1NCA(1NCA;7NN9)	A	E	3329,3067	1953	0.99	0.99
2JEL(2JEL;1POH)	A	E	3297,640	1501	0.92	0.90
1KXP(1IJJ;1KW2)	O	E	2782,3527	3341	0.96	0.97
1IB1 (1QJB;1KUY)	O	MD	3673,1312	2808	0.95	0.87
1WQ1(6Q21;1WER)	O	MD	2534,1351	2913	0.92	0.93
1ATN(1IJJ;3DNI)	O	D	2942,2036	1774	0.95	0.97
1DE4(1A6Z;1CX8)	O	D	3064,1351	2066	0.98	0.97

a) The PDB IDs for the unbound proteins are shown in brackets.
b) The complex category labels taken from the ZDOCK benchmark 2.0. E: enzyme/inhibitor; A: antibody/antigen; O: Others.
c) The prediction difficulty level taken from the ZDOCK benchmark 2.0. E: easy (rigid-body); MD: medium difficulty; D: difficult.
d) The total number of atoms in the receptor and ligand of the unbound forms of the proteins are shown.
e) The change in accessible surface area (calculated using NACCESS) upon complex formation.

ISSN: 1471-2105