Code
Three-dimensional representations of complex carbohydrates and polysaccharides—SweetUnityMol: A video game-based computer graphic software
23/12/14 01:06
SweetUnityMol was just published in Glycobiology (2015) 25 (5): 483-491. doi: 10.1093/glycob/cwu133.
A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein–carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures.
Background: In Nature, carbohydrates form an important family of biomolecules. Carbohydrates, in the form of polysaccharides, glycopeptides, glycolipids, glycosaminoglycans, proteoglycans, or other glycoconjugates have long been recognize to participate in many biological processes. They can be present in very diverse and complex forms. In a similar fashion to proteins with amino acids, we can build complex carbohydrates from individual units: monosaccharides. But whereas the proteic alphabet is made of “only” 20 letters, around 120 monosaccharides are known and the fact that they can be linked through different positions adds even more complexity to the whole construction process.
Methods: Using the molecular visualization software UnityMol engine it is easy to represent proteins, RNA/DNA and biological networks. UnityMol is based on a new molecular representation called HyperBalls[2] properties to draw very large complexes of several thousand atoms without screen lag. based on the Unity3D video game that uses graphical and shader properties to draw very large complexes of several thousand atoms without screen lag.
A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein–carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures.
Background: In Nature, carbohydrates form an important family of biomolecules. Carbohydrates, in the form of polysaccharides, glycopeptides, glycolipids, glycosaminoglycans, proteoglycans, or other glycoconjugates have long been recognize to participate in many biological processes. They can be present in very diverse and complex forms. In a similar fashion to proteins with amino acids, we can build complex carbohydrates from individual units: monosaccharides. But whereas the proteic alphabet is made of “only” 20 letters, around 120 monosaccharides are known and the fact that they can be linked through different positions adds even more complexity to the whole construction process.
Methods: Using the molecular visualization software UnityMol engine it is easy to represent proteins, RNA/DNA and biological networks. UnityMol is based on a new molecular representation called HyperBalls[2] properties to draw very large complexes of several thousand atoms without screen lag. based on the Unity3D video game that uses graphical and shader properties to draw very large complexes of several thousand atoms without screen lag.
UnityMol website goes online
06/03/13 03:35
Hi! Welcome to the brand new UnityMol website designed by Matthieu Chavent and extended by Marc Baaden. We’re excited to bring UnityMol to you and hope you will have fun with the software and also do some exciting research with it. Feedback is always welcome.
