title: Visualisation of cyclic and multi-branched molecules with VMD.
abstract: We report the addition of two visualisation algorithms, termed PaperChain and Twister, to the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce visualisations of complex cyclic molecules and multi-branched polysaccharides and are a generalization and optimization of those we previously developed in a standalone package for carbohydrates. PaperChain highlights each ring in a molecular structure with a polygon, which is coloured according to the ring pucker. Twister traces glycosidic bonds with a ribbon that twists according to the relative orientation of successive sugar residues. Combination of these novel algorithms and new ring selection statements with the large set of visualisations already available in VMD allows for unprecedented flexibility in the level of detail displayed for glycoconjugate, glycoprotein and carbohydrate-binding protein structures, as well as other cyclic structures. We highlight the efficacy of these algorithms with selected illustrative examples, clearly demonstrating the value of the new visualisations, not only for structure validation, but also for facilitating insights into molecular structure and mechanism.
authors.affiliation: Computer Science Department, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa. hodgestar@gmail.com
authors.forename: Simon
authors.initials: S
authors.lastname: Cross
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Kuttel
authors.forename: John E
authors.initials: JE
authors.lastname: Stone
authors.forename: James E
authors.initials: JE
authors.lastname: Gain
mesh_terms: D000465:Algorithms; D006001:Glycoconjugates / Q000737:chemistry; D006023:Glycoproteins / Q000737:chemistry; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009844:Oligosaccharides / Q000737:chemistry
chemical_list: D006001:Glycoconjugates; D006023:Glycoproteins; D009844:Oligosaccharides