Prediction of calcium-binding sites by combining loop-modeling with machine learning

BMC Structural Biology

Table 4 Eight predictions of which their holo structures have been identified through a homologous searching process using MAMMOTH

Protein name	PDB ID	Loop				FEATURE score		Holo structure				Alignement
		Start	End	Sequence	CaDis(Å)	Gap	Loop	SCOP ID	Start	End	CaDis(Å)	PRA	RMSD	PID
CONCANAVALIN A	1APN_A	15	23	TD IGD PSYP	2.40	9.15	58.19	d1vald_	15	23	1.94	99	1.61	96
C-REACTIVE PROTEIN	1LJ7_H	142	149	FGGNFE GS	1.94	-18.56	55.46	d1gnhc_	142	149	1.99	100	0.74	100
SOLUBLE INORGANIC PYROPHOSPHATASE	1IPW_A	97	101	DE AGE	4.67	47.13	53.38	d1i6ta_	97	101	2.19	99	1.49	91
BE TA-KETOACYL REDUCTASE	1I01_C	140	149	VGTMGNGGQA	2.25	7.93	56.74	d1q7bd_	140	149	2.41	96	1.96	89
OBELIN	1SL9_A	122	128	FD KD GSG	1.96	-1.98	50.80	d1sl7a_	122	128	2.43	98	2.89	89
DEOXYRIBONUCLEASE I	2DNJ_A	99	107	D GCE SCGND	2.07	42.69	72.61	d3dnia_	99	107	2.57	100	0.87	98
STAPHYLOCOCCAL NUCLEASE	1SNQ_A	44	51	TKHGKKGV	4.17	45.69	66.14	d1nuca_	44	51	4.88	98	1.70	92
SOLUBLE INORGANIC PYROPHOSPHATASE	1FAJ_A	145	149	E KGKW	3.35	39.95	51.60	d1i40a_	146	149	5.37	99	1.59	87

Column 2 lists protein name that is PDB code followed by the chain identifier. We build structures for gaps of which 3D structures are not present in the original PDB files. Information of these structures, referred as "loop", is given in column 2-5. Column 5 lists the distances from the predicted sites to the rebuilt loops (CaDis). Column 6 and 7 list FEATURE scores at the predicted sites in the structures where loop structures are missing (Gap) and in the rebuilt loop structures (Loop). Ligands observed experimentally are listed in column 8 and the ligand IDs are from PDB. Column 9 shows the SCOP ID of the holo structures. Information of aligned counterparts for the binding loops is listed in column 10-12. Column 12 lists the distances from the calcium ions to the aligned loop counterparts (CaDis). The percentage of residues aligned (PRA), the RMSD of the aligned regions, and the percentage of identical residues (PID) are shown in column 13-15.

ISSN: 1472-6807