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Table 1 Comparison of the chemically relevant alignments of SurfComp and MS3ALIGN.

From: MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature

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

  1. The chemical structures of the ligands are presented in the Additional file 1