title: POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides.
abstract: This article describes an update of POLYS, the POLYSaccharide builder, for generating three-dimensional structures of polysaccharides and complex carbohydrates (Engelsen et al., Biopolymers 1996, 39, 417-433). POLYS is written in portable ANSI C and is now released under an open source license. Using this software, complex branched carbohydrate structures and polysaccharides can be constructed from their primary structure and the relevant monosaccharides stored in database containing information on optimized glycosidic linkage geometries. The constructed three-dimensional structures are described as Cartesian coordinate files which can be used as input to other molecular modeling software. The new version of POLYS includes a large database of monosaccharides and a helical generator to build and optimize regular single helix or double helix structures. To demonstrate the efficiency of POLYS to build carbohydrate structures, four examples of increasing complexity are presented in the manuscript, from simple alpha glucans over complex starch fragments and the double helical structure of amylopectin to the mega-oligosaccharide RhamnoGalacturonan II.
authors.affiliation: Spectroscopy & Chemometrics, Faculty of Science, University of Copenhagen, Rolighedsvej 30, DK-1958 Frederiksberg C, Copenhagen, Denmark.
authors.forename: Søren B
authors.initials: SB
authors.lastname: Engelsen
authors.forename: Peter I
authors.initials: PI
authors.lastname: Hansen
authors.forename: Serge
authors.initials: S
authors.lastname: Pérez
mesh_terms: D000687:Amylopectin / Q000737:chemistry; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D019295:Computational Biology / Q000379:methods*; D005936:Glucans / Q000737:chemistry; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009844:Oligosaccharides / Q000737:chemistry; D010368:Pectins / Q000737:chemistry; D011134:Polysaccharides / Q000737:chemistry*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D005936:Glucans; D009844:Oligosaccharides; D011134:Polysaccharides; C042492:rhamnogalacturonan II; D010368:Pectins; D000687:Amylopectin
keywords: 3D structures; RGII pectin; helical structures; oligosaccharides; polysaccharides; starch