Three-dimensional representations of complex carbohydrates and polysaccharides - SweetUnityMol: A video game-based computer graphic software

Glycobiology

Volumn 25, Issue 5, 2015, Pages 483-491

  Pérez, Serge ^a   Tubiana, Thibault ^b   Imberty, Anne ^c   Baaden, Marc ^b  

^a UNIV GRENOBLE ALPES   (France)

^b France   (France)

^c CENTRE DE RECHERCHES SUR LES MACROMOLÉCULES VÉGÉTALES CERMAV CNRS   (France)

Author keywords

3D visualization; Glycan; Polysaccharides; Software

Indexed keywords

BACTERIAL POLYSACCHARIDE; CARBOHYDRATE; GLYCAN; GLYCOPROTEIN; MONOSACCHARIDE; OLIGOSACCHARIDE; POLYSACCHARIDE; XANTHAN;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; CONFORMATION; MACROMOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CARBOHYDRATE INTERACTION; RECREATION; SWEETUNITYMOL; CHEMISTRY;

CARBOHYDRATE CONFORMATION; CARBOHYDRATES; SOFTWARE; VIDEO GAMES;

EID: 84942258977     PISSN: 09596658     EISSN: 14602423     Source Type: Journal    
DOI: 10.1093/glycob/cwu133     Document Type: Article

References (90)

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2. Berger O, McBride R, Razi N, Paulson J. 2008. Symbol notation extension for pathogen polysaccharides. The Scripps Research Institute, Consortium for Functional Glycomics.
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31. Perez S, Rivet A, Imberty A. 2015. 3D-lectin database. Glycocosci Biol Med. (in press).
32. Perez S, Rodriguez-Carvajal MA, Docco T. 2003. A complex plant cell wall polysaccharide: Rhamnogalacturonan II. A structure in quest of a function? Biochimie. 85: 109-121.
33. Perez S, Vergelati C. 1987. Molecular modelling of the xanthan chain conformations. Int J Biol Macromol. 9: 211-218.
34. Petersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSH chimera - A visualization system for exploratory research and analysis. J Comp Chem. 25: 1605-1612.
35. Richardson JS 1981. The anatomy and taxonomy of protein structure. Adv Protein Chem. 34: 167-218.
36. Rosen J, Miguet L, Perez S. 2009. Shape: Automatic conformation prediction of carbohydrates using a genetic algorithm. J Cheminformatics. 1: 16.
37. Sanner MF 1999. Python: A programming language for software integration and development. J Mol Graph Model. 17: 57-61.
38. Sarkar A, Perez S. 2012. PolySAc3DB: An annotated data base of 3 dimensional structures of polysaccharides. BMC BioInformatics. 13: 302.
39. Simons JP, Davis BG, Cocinero EJ, Gamblin DP, Stanca-Kaposta EC. 2009. Conformational change and selectivity in explicitly hydrated carbohydrates. Tetrahedron Asymmetry. 20: 718-722.
40. Taguchi T, Seko A, Kitajima K, Inoue S, Khoo K-H, Morris HR, Dell A, Inoue Y. 1994. Structural studies of a novel type of pentaantennary large glycan unit in the fertilization-associated carbohydrate-rich glycopeptide isolated from the fertilized eggs of Oryzias latipes. J Biol Chem. 269: 8762-8771.
41. Tarjan R. 1972. Depth-first search and linear graph algorithm. SIAM J Comp. 1: 146-160.
42. Unity3D, http://unity.3d.com, last Accessed December 12, 2014.
43. Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzel ME, editors. 1999. Essentials of Glycobiology. 1st ed. Planview (NY): Cold Spring Harbor Laboratory Press.
44. Wimmerova M, Kozmon S, Necasova I, Mishra SK, Komarek J, Koca J. 2012. Stacking information between carbohydrate and protein quantified by combination of theoretical and experimental methods. PLoS ONE. 7: 46032.
45. Woods R. 2014. GLYCAM Web. Athens (GA): Complex Carbohydrate Research Center, University of Georgia. http://www.glycam.com, last Accessed December 12, 2014.
46. Allen FH 2002. The Cambridge Structural Database: A quarter of a million crystal structures and rising. Acta Cryst. B58: 380-388.
47. Berger O, McBride R, Razi N, Paulson J. 2008. Symbol notation extension for pathogen polysaccharides. The Scripps Research Institute, Consortium for Functional Glycomics.
48. Berman HM, Westbrook J, Feng Z, Gililand G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein Data Bank. Nucleic Acids Res. 28: 235-242.
49. Carson M. 1987. Ribbon models of macromolecules. J Mol Graph. 5: 103-106.
50. Carson M, Bugg C. 1986. Algorithm for ribbon models of proteins. J Mol Graph. 4: 121-122.
51. Chavent M, Vanel A, Tek A, Levy B, Robert S, Raffin B, Baaden M. 2011. GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks and hyperboloids. J Comput Chem. 32: 2924-2935.
52. Chen X, Lu M, Poon BK, Wang Q, Ma J. 2009. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based-X-ray crystallographic refinement. Acta Cryst. D65: 339-347.
53. Consortium for Functional Glycomics. http://www.functionalglycomics.org, last Accessed December 12, 2014.
54. Cross S, Kuttel M, Stone JE, Gain J. 2009. Visualisation of cyclic and multi-branched molecules with VMD. J Mol Graph Model. 28: 131-139.
55. DeLano WL 2002. The PyMol molecular graphics software. DeLano Scientific. http://www.pymol.org.
56. Engelsen SB, Hansen P, Perez S. 2013. POLYS: An open source software package for building three-dimensional structures of polysaccharides. Biopolymers. 101: 733-743.
57. Perez S, Sarkar A, Breton C, Drouillard S, Rivet A, Imberty A. 2013. Glyco3D: A portal for structural glycoscience. http://glyco3d.cermav.cnrs.fr, last Accessed December 12, 2014.
58. Hanson RM 2010. Jmol - A paradigm shift in crystallographic visualization. J Appl Crystallogr. 43: 1250-1260.
59. Humphrey W, Dalke A, Schulten K. 1996. VMD-visual molecular dynamics. J Mol Graph. 14: 33-58.
60. Imberty A, Chanzy H, Perez S, Buleon A, Tran V. 1988. The double helical nature of A-starch. J Mol Biol. 201: 365-378.
61. Imberty A, Gautier C, Lescar J, Perez S, Wyns L, Loris R. 2000. An usual carbohydrate binding site revealed by the structures of two Maakia amurensis lectins complexed with sialic acid containing oligosaccharides. J Biol Chem. 275: 17541-17548.
62. Imberty A, Perez S. 1988. A revisit to the three-dimensional structure of B-amylose. Biopolymers. 27: 1205-1221.
63. Johnson G, Hertig S. 2014. A guide to the visual analysis and communication of biomolecular structural data. Nat Rev. 15: 690-698.
64. Kamerling JP 2007. Basic concepts and nomenclature recommendations incarbohydrate chemistry. In: Kamerling JP, editor. Comprehensive Glycosciences, from Chemistry to System Biology. Oxford: Elsevier. Vol. 1, p. 1-37.
65. Kuttel M, Gain J, Burger A, Eborn E. 2006. Techniques for visualization of carbohydrate molecules. J Mol Graph Model. 25: 380-388.
66. Kuttel M, Mao Y, Widmalm G, Lundborg M. 2011. CarbBuilder: An adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation. Seventh IEEE International Conference on eScience, Stockholm, Sweden, p. 395-402.
67. Lütteke T. 2009. Analysis and validation of carbohydrate three-dimensional structures. Acta Cryst D. 65: 156-168.
68. Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth C-W. 2006. GLYCOSCIENCES.de: An Internet portal to support glycomics and glycobiology research. Glycobiology. 16: 71R-81R.
69. Lv Z, Tek A, Da Silva F, Empereurmot C, Chavent M, Baaden M. 2013. Game on, science - How video game technology may help biologists tackle visualization challenges. PLoS ONE. 8: e57990.
70. McNaught AD 1997. Nomenclature of carbohydrates (Recommendations 1996). Adv Carbohydr Chem Biochem. 52: 43-177.
71. Nakahara T, Hashimoto R, Nakagawa H, Monde K, Miura N, Nishimura SI. 2008. Glycoconjugate data bank structure - an associated database and N-glycan primary structure verification service. Nucleic Acid Res. 36: D368-D371.
72. Pendrill R, Jonsson KHM, Widmalm G. 2013. Glycan synthesis, structure and dynalics: A selection. Pure Appl. Chem. 85: 1759-1770.
73. Perez S. 2007. Oligosaccharides and polysaccharides by diffraction methods. In: Kamerling JP, editor. Comprehensive Glycosciences, Analytical Aspects (Scope and Limitations). Oxford: Elsevier. Vol. 2, p. 347-387.
74. Perez S. 2014. The symbolic representation of monosaccharides in the age of glycobiology, http://glycopedia.eu, last Accessed December 12, 2014.
75. Perez S, Gautier C, Imberty A. 2000. Oliogosaccharides by diffraction methods. In: Ernst B, Hart GW, Sinay P, editors. Oligosaccharides in Chemistry- and Biology. Weinheim: Wiley-VCH Verlag GmbH. p. 969-1001.
76. Perez S, Rivet A, Imberty A. 2015. 3D-lectin database. Glycocosci Biol Med. (in press).
77. Perez S, Rodriguez-Carvajal MA, Docco T. 2003. A complex plant cell wall polysaccharide: Rhamnogalacturonan II. A structure in quest of a function? Biochimie. 85: 109-121.
78. Perez S, Vergelati C. 1987. Molecular modelling of the xanthan chain conformations. Int J Biol Macromol. 9: 211-218.
79. Petersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSH chimera - A visualization system for exploratory research and analysis. J Comp Chem. 25: 1605-1612.
80. Richardson JS 1981. The anatomy and taxonomy of protein structure. Adv Protein Chem. 34: 167-218.
81. Rosen J, Miguet L, Perez S. 2009. Shape: Automatic conformation prediction of carbohydrates using a genetic algorithm. J Cheminformatics. 1: 16.
82. Sanner MF 1999. Python: A programming language for software integration and development. J Mol Graph Model. 17: 57-61.
83. Sarkar A, Perez S. 2012. PolySAc3DB: An annotated data base of 3 dimensional structures of polysaccharides. BMC BioInformatics. 13: 302.
84. Simons JP, Davis BG, Cocinero EJ, Gamblin DP, Stanca-Kaposta EC. 2009. Conformational change and selectivity in explicitly hydrated carbohydrates. Tetrahedron Asymmetry. 20: 718-722.
85. Taguchi T, Seko A, Kitajima K, Inoue S, Khoo K-H, Morris HR, Dell A, Inoue Y. 1994. Structural studies of a novel type of pentaantennary large glycan unit in the fertilization-associated carbohydrate-rich glycopeptide isolated from the fertilized eggs of Oryzias latipes. J Biol Chem. 269: 8762-8771.
86. Tarjan R. 1972. Depth-first search and linear graph algorithm. SIAM J Comp. 1: 146-160.
87. Unity3D, http://unity.3d.com, last Accessed December 12, 2014.
88. Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzel ME, editors. 1999. Essentials of Glycobiology. 1st ed. Planview (NY): Cold Spring Harbor Laboratory Press.
89. Wimmerova M, Kozmon S, Necasova I, Mishra SK, Komarek J, Koca J. 2012. Stacking information between carbohydrate and protein quantified by combination of theoretical and experimental methods. PLoS ONE. 7: 46032.
90. Woods R. 2014. GLYCAM Web. Athens (GA): Complex Carbohydrate Research Center, University of Georgia. http://www.glycam.com, last Accessed December 12, 2014.