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Table 4 Comparison of LIGSITEcsc, LIGSITE, PASS, SURFNET, CAST on 48 unbound structures.

From: LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation

Complex Unbound LIGSITEcsc 1 LIGSITE2 PASS3 SURFNET4 CAST
  PDB Hits5 D Near 6 Hits D Near Hits D Near Hits7 D Near Hits D Near
1bid 3tms 1 3.4 1 2.0 1 3.9 1 3.9 1 3.1
1cdo 8adh 1 0.8 1 0.6 1 0.2 1 1.3 1 0.8
1dwd 1hxf 1 1.7 1 2.3 1 0.7 1 2.3 1 0.9
1fbp 2fbp 1 0.5 1 0.6 (2) 0.8 - - 1 1.5
1gca 1gcg 1 0.8 1 0.8 1 0.5 1 3.4 1 0.5
1hew 1hel 1 1.8 1 1.8 1 1.0 1 2.6 1 1.6
1hyt 1npc 1 1.2 1 1.1 1 1.7 1 1.0 1 0.7
1inc 1esa 1 2.9 3 0.8 - - 1 1.9 (10) 2.1
1rbp 1brq 1 0.9 1 0.9 1 0.9 (2) 1.6 1 1.0
1rob 8rat 1 0.9 2 1.0 1 0.3 1 1.7 1 1.6
1stp 1swb 1 0.6 1 0.3 1 0.8 1 2.4 1 1.4
1ulb 1ula - - (20) 3.2 - - 1 3.6 1 3.3
2ifb 1ifb 1 2.2 1 2.2 1 2.5 1 2.3 1 2.1
3ptb 3ptn 1/2 1.1 2 1.0 (2) 0.5 (2) 1.7 1 0.9
2ypi 1ypi - 3.0 2 3.0 (3) 2.2 - - (2) 2.7
4dfr 5dfr 1 1.9 1 3.5 1 2.3 - - 1 4.5
4phv 3phv 1 2.7 1 2.6 - - 1 2.9 1 2.6
5cna 2ctv 1/11 1.0 (13) 1.0 (2) 0.8 (6) 1.1 (6) 1.0
7cpa 5cpa 1 1.0 1 1.1 1 1.3 1 1.6 (3) 1.0
1a6w 1a6u 1/3 0.5 (4) 1.4 - - - - 1 1.4
1acj 1qif - 3.5 - 3.6 1 1.9 - - (40) 3.9
1apu 3app - 1.2 - 1.9 - - 1 3.7 -(2) -(4.1)
1blh 1djb 1 0.7 2 1.2 1 2.4 (2) 3.9 (5) 0.8
1byb 1bya 1 2.5 1 2.8 (4) 1.1 -1 -(4.2) 1 2.4
1hfc 1cge 1 0.7 1 0.9 (3) 0.8 (3) 1.2 1 0.5
1ida 1hsi 1 3.4 1 2.9 (3) 1.0 1 1.0 1 1.6
1igj 1a4j /4 0.8 -(19) 2.9 - - - - - -
1imb 1ime 1 1.7 1 1.0 1 1.7 1 4.0 1 1.3
1ivd 1nna 1 1.4 1 1.1 1 3.5 (2) 0.9 1 1.9
1mrg 1ahc 1 1.9 1 1.9 - - 1 3.3 1 0.8
1mtw 2tga 1/5 2.8 -(7) 1.2 - - (7) 3.2 (8) 1.6
1okm 4ca2 1 2.2 1 1.6 - - (3) 2.2 1 2.1
1pdz 1pdy 1 2.6 1 3.1 1 1.7 - - (5) 1.0
1phd 1phc 1 0.7 1 1.2 1 1.8 (2) 1.4 1 1.3
1pso 1psn 1 0.8 1 1.6 1 1.6 -1 -(4.3) 1 2.1
1qpe 3lck 2 1.5 2 1.2 1 0.7 - - - -
1rne 1bbs 1 1.0 1 1.2 1 1.4 1 2.2 1 1.0
1snc 1stn 1 1.5 1 1.5 1 1.3 1 1.9 1 1.3
1srf 1pts 1 1.5 1 0.5 1 1.2 (5) 0.8 1 1.1
2ctc 2ctb 1 0.6 1 1.1 (2) 0.8 1 2.2 1 1.2
2h4n 2cba 1/2 1.0 2 1.0 - - (3) 1.2 (2) 1.2
2pk4 1krn 1/2 0.7 2 0.8 - - (2) 2.2 1 1.9
2sim 2sil 1/2 0.7 2 0.6 - - (2) 2.3 (2) 0.8
2tmn 1l3f - 2.1 - - - - 1 0.7 1 3.9
3gch 1chg 10 2.2 -(10) 2.2 1 0.9 (11) 1.5 (2) 2.5
3mth 6ins 9 3.8 -(9) 1.8 - - -(3) -(4.7) - -
5p2p 3p2p 1 1.3 1 1.6 1 1.8 (2) 1.6 (2) 1.5
6rsa 7rat 1/4 0.9 -(5) 1.1 1 1.1 1 0.6 1 0.9
  1. 1Grid resolution: 1.0 Å; probe radius: 1.6 Å.
  2. 2Parameters are the same as LIGSITEcsc.
  3. 3The values are directly taken from PASS [9]. Only the best hit is shown.
  4. 4Grid separation: 1.0 Å. Minimum and maximum radius for gap spheres: 1.0 and 4.0 Å. The "gaps.pdb" file is used for representation for pocket sites.
  5. 5Hits: PS(s) lying within 4 Å of the superimposed ligand. Only the best hit is shown. A dash indicates that no hit is found, brackets indicate hits, which are no top hits.
  6. 6Distances from hits to the nearest atom of superimposed ligand, unit: Å.
  7. 7PS(s) lying within 4 Å of the superimposed ligand.