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

BMC Structural Biology

Table 5 14 FEATURE predictions of which experimentally solved homologous holo structures are found through a homologous searching process using MAMMOTH

	Loop				FEATURE score			Holo structure				Alignement
PDB ID	Start	End	Sequence	CaDis(Å)	Gap	Loop	Ligand	SCOP ID	Start	End	Sequence	CaDis(Å)	PRA	RMSD	PID
1G57_B	33	39	DDED RE N	2.29	-29.15	62.92	CS	d1pvwa_	21	27	D SDE RE G	2.11	86	2.65	24
1VJS_A	181	193	AWD WE VSNE NGNY	2.49	41.99	82.70	None	d1e40a2	178	193	E GKAWD WE VSSE NGNYD YLMY	2.18	97	1.06	66
2A9Q_A	53	59	LMLPE ID	3.34	44.10	57.51	None	d1zh2b1	53	59	LGLPD GD	2.23	98	1.34	41
1GIH_A	149	164	ARAFGVPVRTYTHE VV	3.16	37.28	60.16	1PU	d1u5ra_	173	184	ASIMAPANFVG	2.47	81	3.03	19
1OZT_G	127	141	GKGGNEE STKTGNAG	1.71	23.67	61.66	None	d1sxsb_	125	139	GRGGNEE STKTGNAG	3.53	87	1.86	71
1LEW_A	173	183	RHTDDE MTGYV	2.20	10.16	71.76	None	d2eufb1	170	180	YSFQMALTSVV	4.18	85	2.92	25
2JAV_A	131	141	SD GGHTVLHRD	2.60	8.93	56.86	5Z5	d2auha1	1123	1132	LNAKKFVHRD	4.87	85	3.06	16
2ANT_I	29	43	KATEDE GSE QKIPE A	2.23	20.71	80.94	NAA	d1jmja_	68	99	SEDD LQLFH	5.09	92	2.31	26
1U5I_A	563	568	KRED IK	2.97	39.39	66.52	None	d1alwb_	127	133	TRHPD LK	5.37	98	1.82	13
1EB7_A	222	229	ASVLPSGD	3.96	19.22	58.45	CA,HEC	d1iqca2	207	213	E TKNPAA	6.58	86	1.79	21
1ANT_L	395	406	LNPNRVTFKANR	2.95	42.78	77.77	None	d1jmja_	446	454	TQVRFTVD R	6.64	88	2.72	26
2IYN_C	84	97	ARGEEED RVRGLE T	3.26	35.10	52.26	MG	d1srrc_	81	96	MTAYGE LD MIQE SKE L	6.88	96	2.7	25
2IK4_A	103	113	PNVSHPE TKAV	3.95	41.81	64.20	MG,PO4,	d1i40a_	59	63	NHTLS	4.03	91	3.49	13

Column 1 lists 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 homologous holo structures. Information of aligned counterparts for the binding loops is listed in column 10-13. Column 13 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 14-16.

ISSN: 1472-6807