LINUCS was chosen to fulfil to following conditions:
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Input: | A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC |
Output: | A linear, unique notation |
LINUCS: LInear Notation for Unique description of Carbohydrate Sequences
Introduction
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Saccharide taken from CarbBank |
a-D-Manp-(1-2)-a-D-Manp-(1-6)+ | a-D-Manp-(1-6)+ | | a-D-Manp-(1-2)-a-D-Manp-(1-3)+ b-D-Manp-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-Asn | a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ |
Variation 1 |
a-D-Manp-(1-2)-a-D-Manp-(1-3)+ |
Variation 2 |
a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ |
Variation 3 |
a-D-Manp-(1-2)-a-D-Manp-(1-2)-a-D-Manp-(1-3)+ |
Description: |
Dorland L; van Halbeek H; Vliegenthart JFG; Lis H; Sharon Primary structure of the carbohydrate chain of soybean agglutinin. A reinvestigation by high-resolution 1H-NMR spectroscopy J Biol Chem (1981) 256: 7708-7711 |
In the example you can see four times the same chemical structure but with another notation. Only the following notation can describe the structure unique:
The first step is to transform the carbohydrate in SWEET-notation and [][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{In a tab'd writing you can see the nested structure better: [][Asn]{The blue marked connections are points where the sorting makes the structure unique. The structure starts with the reducing end. This is the same point where nature starts building the complex carbohydrate structure. It garantes the there is only one end.
You can transform the structure back to IUPAC nomenclature by reversing the structure. In this case |
References
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When citing LINUCS, please refer to:
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