lgsdataset | Plant Macromolecules Research Group

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Lignin structure (LGS) Dataset

About

LGS Dataset enumerates lignin chains for degree of polymerization ranging 3 to 25 following published monomer coupling feasibility rules. The dataset includes two types of lignin library with 60K polymer structures of milled wood lignin.

G type lignin structures which represent spruce MWL structures with 6.3K polymers
SG type lignin structures which represent birch MWL structures with 53.7K polymers

Download

You can download the databases using the links below. All the molecules are stored in canonized SMILES format and molecular data file (*.mol) compressed as zip archive. To see the structures in drawing format, we suggest any chemical structure viewer that can be visualized using SMILES / SDF files such as ChemDraw online for 2D structure and Avogadro for 3D visualization.

Terms of use: The LGS dataset may be downloaded free from here and figshare. In published research involving LGS, cite the appropriate references mentioned below.

Dataset type	Description	Link	Size
G Type Structures	TMAP Visualization
Molecular data file (*.mol)	Chemical structure file format, supported in most of molecular dynamics’ software	MOL File	14.2MB
Connectivity and adjacency matrices (*.csv)	Matrices defining monomer connectivity	Metrices	3MB
Comprehensive dataset (*.json)	Structural definition of all possible sequence in SMILES representation, evaluation structural features such as molecular weight, functional group count and bond proportion of simulated structures	JSON File	216KB
S/G Type Structures	TMAP Visualization
Molecular data file (*.mol)	Chemical structure file format, supported in most of molecular dynamics’ software	MOL File	140MB
Connectivity and adjacency matrices (*.csv)	Matrices defining monomer connectivity	Matrices	26.5MB
Comprehensive dataset (*.json)	Structural definition of all possible sequence in SMILES representation, evaluation structural features such as molecular weight, functional group count and bond proportion of simulated structures	JSON File	2.3MB

Citation

Eswaran, S. c. d., Subramaniam, S., Sanyal, U., Rallo, R. & Zhang, X. Molecular structural dataset of lignin macromolecule elucidating experimental structural compositions. Scientific Data 9, 647, doi:10.1038/s41597-022-01709-4 (2022)

Lignin Structure Generator Tool & Usage

Molecular structure simulation tool for lignin macromolecule. Lignin structure generator uses sequence-controlled structure generation approach for generating polymer chains of length 3 to 25. Workflow includes following functionalities

a) Sequencing of lignin monomers and conditional linkage generation
b) Generating the topological matrices and directed graph representation
c) Converting the directed graphs into molecular structures
d) Validation the dataset against the experimental observations and simulated structures from previous studies
e) Storing the valid structures forming a dataset

The installation and use of the source code can be found from the GitHub repository (https://github.com/sudhacheran/lignin-structure-generator)

For further details, please contact: x.zhang@wsu.edu