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POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides.
Søren B Engelsen1, Peter I Hansen, Serge Pérez
1Spectroscopy & Chemometrics, Faculty of Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Copenhagen, Denmark.
Biopolymers
|December 3, 2013
Summary
The POLYSaccharide builder (POLYS) software has been updated for creating 3D structures of complex carbohydrates and polysaccharides. This open-source tool aids in visualizing intricate molecular architectures for research.
Area of Science:
- Carbohydrate Chemistry
- Computational Biology
- Structural Bioinformatics
Background:
- Accurate three-dimensional (3D) structure generation is crucial for understanding polysaccharide and complex carbohydrate function.
- Existing tools may lack comprehensive databases or the ability to model complex branched structures.
Purpose of the Study:
- To introduce an updated version of the POLYSaccharide builder (POLYS) software.
- To enhance capabilities for generating 3D structures of diverse carbohydrate molecules.
- To provide an open-source tool for computational carbohydrate research.
Main Methods:
- Utilizing a portable ANSI C-based software, POLYS.
- Employing a database of monosaccharides with optimized glycosidic linkage geometries.
- Incorporating a helical generator for regular helix structures.
Main Results:
- POLYS can construct complex branched carbohydrate structures and polysaccharides from primary sequence data.
- Generated 3D structures are output as Cartesian coordinate files compatible with molecular modeling software.
- Demonstrated efficiency with examples including alpha-glucans, starch fragments, amylopectin, and RhamnoGalacturonan II.
Conclusions:
- The updated POLYS software is an efficient, open-source tool for building complex carbohydrate 3D structures.
- Its comprehensive database and modeling capabilities support advanced research in glycobiology.
- Facilitates the study of polysaccharide structure-function relationships through computational modeling.
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