Table 1.
Comparison of the chemically relevant alignments of SurfComp and MS3ALIGN.
| Ligand pair | SURFCOMP aligns | MS3ALIGN aligns |
|---|---|---|
| 1THL-1TLP | Tryptophan moiety | Tryptophan moiety |
| 1THL-1TMN | Tryptophan moiety | Benzyl moiety |
| Tryptophan moiety (6th best) | ||
| 1THL-3TMN | Tryptophan moiety | – |
| 1TLP-1TMN | Tryptophan moiety | Tryptophan moiety |
| 1TLP-3TMN | Tryptophan moiety | – |
| 1TMN-3TMN | Tryptophan moiety | – |
| 4TMN-5TLN | – | Benzyl moiety |
| 4TMN-5TMN | L-Alanine moiety | L-Alanine moiety |
| 4TMN-6TMN | L-Alanine moiety | L-LAanine moiety |
| 5TLN-5TMN | – | Benzyl moiety |
| 5TLN-6TMN | – | Benzyl moiety |
| 5TMN-6TMN | 4-methyl pentanoic | 4-methyl pentanoic acid group |
| acid group | ||
| FOL-TOP | – | – |
| FOL-MTX | Entire ligands | Entire ligands |
| FOL-WRB | Benzyl moiety | C =N−C= N part of triazine and |
| pteridine groups along with amino | ||
| groups | ||
| TOP-MTX | – | C =N−C= N part of triazine and |
| pteridine groups along with amino | ||
| groups | ||
| TOP-WRB | – | C =N−C= N part of triazine and |
| pteridine groups along with amino | ||
| groups | ||
| MTX-WRB | – | C =N−C= N part of triazine and |
| pteridine groups along with amino | ||
| groups |
The chemical structures of the ligands are presented in the Additional file 1