Skip to main content

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

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

PDB1_LIG1 PDB2_LIG2 ProFunc SuMo SitesBase PocketMatch PyMol
   Score E- value   Score/Max.score = Ratio PI PMScoreMin 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
  1. PMScore and PMScore min refer 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.