olivierclerc/convert-glycoct-inp

Script for converting GlycoCT format to INP. Just for GAG for now.

convert-glycoct-inp

This work is part of MatrixDB project.

This script in perl converts Glycosaminoglycans (GAGs) in GlycoCT format to INP format. The output is then used by POLYS tool to create 3D structure in PDB format.

This script takes as args a CSV file and a GlycoCT file. It prints on stdout the corresponding INP format for POLYS tool.

Important to know

• This script doesn't support ALT, UND and ISO sections of GlycoCT
• This script support REP sections but not nested repetitions
• This script only converts GAG's monosaccharides
• In order to build a 3D structure, POLYS need to have all information about monosaccharides: alpha/beta, L/D, etc...
• Iduronic acid can have many conformations (1C4, 4C1, 2S0). We have not this information in GlycoCT format but we need it for POLYS. Thus we decided to choose 1C4 conformation by default.

Example of use:

    perl convertor2.0.pl phi_psi_all_disacc.csv HP_dp02_0001.glycoct > HP_dp02_0001.inp

• convertor2.0.pl is the script in perl
• phi_psi_all_disacc.csv is the CSV file in which we have phi and psi values of GAG's disaccharides
• HP_dp02_0001.glycoct is a GlycoCT file of disaccharide of heparin

convert-glycoct-inp's Issues

non accessible code

to whom it may concerns,

I want to create the structure of dermatan sulfate
I tried with the example code posted in your publication, but it didn't work

---

RES
1r:r1
REP
REP1:4o(4+1)2d=50-150
RES
2b:b-dgal-HEX-1:5
3s:n-acetyl
4a:a1
5s:sulfate
6s:sulfate
LIN
1:2d(2+)3n
2:2o(3+1)4d
3:2o(4+1)5n
4:2o(6+1)6n
ALT
ALT1
ALTSUBGRAPH1
LEAD-IN RES:7
RES
7b:b-dglc-HEX-1:5|6:a
8s:sulfate
LIN
5:7o(2+1)8n
ALTSUBGRAPH2
LEAD-IN RES:9
RES
9b:a-lido-HEX-1:5|6:a
10s:sulfate
LIN
6:9o(2+1)10n

---

After a long search, I finally found dermatan sulfate under the ID G00019MO in the glytoucan DB, but unfortunately the corresponding GlycoCt code does not exist in you library.

---

RES
1b:x-dgal-HEX-x:x
2s:n-acetyl
3b:b-dido-HEX-1:5|6:a
4b:b-dgal-HEX-1:5
5s:n-acetyl
6b:b-dido-HEX-1:5|6:a
7s:sulfate
8s:sulfate
LIN
1:1d(2+1)2n
2:1o(3+1)3d
3:3o(4+1)4d
4:4d(2+1)5n
5:4o(3+1)6d
6:4o(4+1)7n
7:1o(4+1)8n

---

Please can you fix this, knowing that this structure for me is the only and the last solution to have sulfate groups on dermatan sulfate.

Thank you very much for your help.
Cordially,

Islem HABIBI