Glycan Alignment

Last update: 06/30/2016

Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.

1. Installation

Click here to download the GS-align software package including example PDB glycan structures.

The source code of GS-align (gsalign.cpp) is written in C++ and can be easily compiled using C++ GNU compiler by

>g++ -c gsalign.cpp
>g++ -o gsalign gsalign.o

2. Preparing input glycan structures

Input glycan structure files for GS-align must be in PDB format and be ended with "TER". Users can prepare an input structure by manually extracting the glycan coordinate data from a PDB file. We also recommend use of Glycan Reader (, which is our web-based tool for automated glycan identification and simulation preparation (Jo et al. J. Comput. Chem. 2011, 32: 3135-3141).

GS-align needs information on which glycosidic oxygen is linked to which residue for the calculation of GS-score. However, it is not easy to manually assign the glycosidic oxygen information only based on the context in the PDB file. The GS-align software package contains an auxiliary program ( to automatically assigned the glycosidic oxygens after renumbering the residue sequences.

>javac (for compile)
>java AssignOGAtoms [glycan structure file in PDB format] (for execution)

3. Running GS-align


glycan structure 1 (PDB format)


glycan structure 2 (PDB format)


GS-score normalization option (default = 1)
    1: normalize using larger glycan
    2: normalize using smaller glycan
    3: normalize using -s1 structure


output option (default = 1)
    1: score only
    2: score, superposed -s2 structure with matrix, and sequence alignment

(Example) >gsalign -s1 1L6X_A_glycan_OG.pdb -s2 4KU1_B_glycan_OG.pdb -n 1 -o 2

4. Outputs


calculated using all aligned residue pairs


calculated using aligned residue pairs within 5 Å


the PDB coordinates of -s2 structure aligned onto -s1 structure


translational and rotational matrix to align -s2 structure onto -s1 structure

Seq. Alignment

a list of -s2 residues aligned onto -s1 residues within 5 Å