PocketMatch: A new algorithm to compare binding sites in protein structures

BMC Bioinformatics

Table 2 Comparison of PocketMatch with other site matching algorithms- ProFunc, SuMo, SitesBase and PyMol

PDB1_LIG1	PDB2_LIG2	ProFunc		SuMo	SitesBase		PocketMatch		PyMol
		Score	E- value		Score/Max.score = Ratio	PI	PMScore_Min	PMScore	#R	rmsd
Pairs of proteins belonging to same SCOP families
1DHJ_MTX	4DFR_MTX	112	0.745	100	65/78 = 83.33	0	85.25	85.25	13,14,14	0.231
1A4G_ZMR	1NSC_SIA	112	0.277	76	74/79 = 93.67	0	99.91	88.39	16,16,17	0.141
1SDU_MK1	1SDT_MK1	X	-	NA	111/111 = 100	0	98.93	91.23	25,25,26	0.298
1B42_SAH	2VP3_SAH	241	9.8E- 4	91	100/130 = 76.92	0	99.4	89.29	19,20,19	0.088
1GJC_130	1V2Q_ANH	229	0.018	89	52/177 = 29.38	3E- 28	93.65	50.17	12,17,13	0.294
	2AYW_ONO	217	6.66E- 04	40	NA	-	56.9	52.29	15,17,17	1.186
	1O3P_655	X	-	NA	97/177 = 54.80	0	100	88.01	16,17,16	0.113
1ADD_1DA	2ADA_HPR	150	0.151	45	67/72 = 93.06	0	94.72	83.59	14,16,17	0.149
1KV5_PGA	2JGQ_PO4	104.586	23.327	X	NA	-	80.48	28.40	6,13,8	3.527
1BZC_TPI	1GFY_COL	174	0.176	27	57/95 = 60	2.4E- 40	96.87	75.41	12,15,13	0.236
1DJX_I3P	1DJY_I2P	X	-	58	46/53 = 86.79	2.5E- 38	100	69.05	10,10,12	0.160
1AJ6_NOV	1EI1_ANP	102	0.620	X	30/54 = 55.55	7.6E009	91.53	21.16	6,11,24	3.019
Pairs of proteins belonging to different SCOP families
1ECM_TSA	4CSM_TSA	X	-	X	47/86 = 54.65	8.6E- 27	74.22	55.56	10,15,13	0.640
1M6Z_HEC	1LGA_HEM	X	-	X	X	-	67.58	63.85	12,23,24	5.875
1ZID_ZID	2CIG_1DG	X	-	NA	NA	-	58.94	56.01	5,27,29	5.691
1V07_HEM	1HBI_HEM	X	-	X	44/94 = 46.81	2.6E- 16	68.94	61.42	7,18,17	0.690

PMScore and PMScore_minrefer to PocketMatch scores with the two metrics described in the text. Scores for ProFunc, SuMo and SitesBase are as obtained individually from their respective web servers. Significance values where available are also indicated. SitesBase scores refer to number of matches (atoms)/maximum number of matches possible (total number of atoms present) = Percentage of atoms matched. PyMol (#R) refers to number of residues matched, number of residues in Site1, number of residues in Site2. X refers to cases where similarities are not detected with default settings of the algorithm, while NA indicates non availability that PDB entry in that dataset.

ISSN: 1471-2105