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 | 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 |
PMScore and PMScoremin 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.