메뉴 건너뛰기




Volumn , Issue , 2011, Pages 395-402

CarbBuilder: An adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation

Author keywords

CarbBuilder; carbohydrate; CASPER; molecular simulation; molecular strucutre; polysaccharides; psfgen

Indexed keywords

CARBBUILDER; CASPER; MOLECULAR SIMULATIONS; MOLECULAR STRUCUTRE; PSFGEN;

EID: 84856342751     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/eScience.2011.61     Document Type: Conference Paper
Times cited : (28)

References (37)
  • 1
    • 80052026553 scopus 로고    scopus 로고
    • Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins
    • S. Jo, K. C. Song, H. Desaire, A. D. MacKerell, Jr., and W. Im, "Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins," J. Comput. Chem., vol. 32, pp. 3135-3141, 2011.
    • (2011) J. Comput. Chem. , vol.32 , pp. 3135-3141
    • Jo, S.1    Song, K.C.2    Desaire, H.3    MacKerell Jr., A.D.4    Im, W.5
  • 2
    • 33646160614 scopus 로고    scopus 로고
    • GLYCOSCIENCES.de: An internet portal to support glycomics and glycobiology research
    • T. Lütteke, A. Bohne-Lang, A. Loss, T. Goetz, and C. von der Lieth, "GLYCOSCIENCES.de: an internet portal to support glycomics and glycobiology research," Glycobiology, vol. 16, pp. 71R-81R, 2006.
    • (2006) Glycobiology , vol.16
    • Lütteke, T.1    Bohne-Lang, A.2    Loss, A.3    Goetz, T.4    Von Der Lieth, C.5
  • 3
    • 84856333839 scopus 로고    scopus 로고
    • July. [Online]. Available
    • (2005-2011, July). [Online]. Available: http://www.glycam.com
    • (2005)
  • 4
    • 35648968070 scopus 로고    scopus 로고
    • Visualization software for molecular assemblies
    • T. D. Goddard and T. E. Ferrin, "Visualization software for molecular assemblies," Curr. Opin. Struc. Biol., vol. 17, pp. 587-595, 2007.
    • (2007) Curr. Opin. Struc. Biol. , vol.17 , pp. 587-595
    • Goddard, T.D.1    Ferrin, T.E.2
  • 5
    • 0030248409 scopus 로고    scopus 로고
    • A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates
    • S. B. Engelsen, S. Cros, W. Mackie, and S. Pérez, "A molecular builder for carbohydrates: Application to polysaccharides and complex carbohydrates," Biopolymers, vol. 39, no. 3, pp. 417-433, 1996.
    • (1996) Biopolymers , vol.39 , Issue.3 , pp. 417-433
    • Engelsen, S.B.1    Cros, S.2    Mackie, W.3    Pérez, S.4
  • 6
    • 74049121217 scopus 로고    scopus 로고
    • Shape: Automatic conformation prediction of carbohydrates using a genetic algorithm
    • J. Rosen, L. Miguet, and S. Pérez, "Shape: automatic conformation prediction of carbohydrates using a genetic algorithm," Journal of Cheminformatics 2009, 1:16, vol. 1, no. 16, 2009.
    • (2009) Journal of Cheminformatics 2009, 1:16 , vol.1 , Issue.16
    • Rosen, J.1    Miguet, L.2    Pérez, S.3
  • 7
    • 79952164219 scopus 로고    scopus 로고
    • Structure analysis of glycans by nmr chemical shift prediction
    • M. Lundborg and G. Widmalm, "Structure analysis of glycans by nmr chemical shift prediction," Anal. Chem., vol. 83, pp. 1514-1517, 2011.
    • (2011) Anal. Chem. , vol.83 , pp. 1514-1517
    • Lundborg, M.1    Widmalm, G.2
  • 8
    • 33646153281 scopus 로고    scopus 로고
    • Sequence determination of oligosaccharides and regular polysaccharides using nmr spectroscopy and a novel web-based version of the computer program casper
    • P.-E. Jansson, R. Stenutz, and G. Widmalm, "Sequence determination of oligosaccharides and regular polysaccharides using nmr spectroscopy and a novel web-based version of the computer program casper,"Carbohydr. Res., vol. 341, pp. 1003-1010, 2006.
    • (2006) Carbohydr. Res. , vol.341 , pp. 1003-1010
    • Jansson, P.-E.1    Stenutz, R.2    Widmalm, G.3
  • 9
    • 33750073184 scopus 로고    scopus 로고
    • Techniques for visualization of carbohydrate molecules
    • M. Kuttel, J. Gain, A. Burger, and I. Eborn, "Techniques for visualization of carbohydrate molecules," J. Mol. Graphics Modell., vol. 25, pp. 380-388, 2006.
    • (2006) J. Mol. Graphics Modell. , vol.25 , pp. 380-388
    • Kuttel, M.1    Gain, J.2    Burger, A.3    Eborn, I.4
  • 10
    • 70349329514 scopus 로고    scopus 로고
    • Visualisation of cyclic and multi-branched molecules with vmd
    • S. Cross, M. M. Kuttel, J. E. Stone, and J. E. Gain, "Visualisation of cyclic and multi-branched molecules with vmd," J. Mol. Graphics Modell., vol. 28, pp. 131-139, 2009.
    • (2009) J. Mol. Graphics Modell. , vol.28 , pp. 131-139
    • Cross, S.1    Kuttel, M.M.2    Stone, J.E.3    Gain, J.E.4
  • 11
    • 37849189530 scopus 로고    scopus 로고
    • Nomenclature of carbohydrates (recommendations 1996)
    • A. D. McNaught, "Nomenclature of carbohydrates (recommendations 1996)." Adv. Carbohydr. Chem. Biochem,, vol. 52, pp. 43-177, 1997.
    • (1997) Adv. Carbohydr. Chem. Biochem , vol.52 , pp. 43-177
    • McNaught, A.D.1
  • 12
    • 0024201741 scopus 로고
    • Conformational analysis and molecular dynamics simulations of maltose
    • S. N. Ha, L. J. Madsen, and J. W. Brady, "Conformational analysis and molecular dynamics simulations of maltose," Biopolymers, vol. 27, pp. 1927-1952, 1988.
    • (1988) Biopolymers , vol.27 , pp. 1927-1952
    • Ha, S.N.1    Madsen, L.J.2    Brady, J.W.3
  • 13
    • 0000085348 scopus 로고
    • Comparisons of rigid and relaxed conformational maps of maltose and cellobiose
    • A. D. French, "Comparisons of rigid and relaxed conformational maps of maltose and cellobiose," Carbohydr. Res., vol. 188, pp. 206-211, 1989.
    • (1989) Carbohydr. Res. , vol.188 , pp. 206-211
    • French, A.D.1
  • 14
    • 0027109492 scopus 로고
    • Conformational analysis of the anomeric forms of sophorose, laminarabiose and cellobiose using MM3
    • M. K. Dowd, A. D. French, and P. J. Reilly, "Conformational analysis of the anomeric forms of sophorose, laminarabiose and cellobiose using MM3," Carbohydr. Res., vol. 233, pp. 15-34, 1992.
    • (1992) Carbohydr. Res. , vol.233 , pp. 15-34
    • Dowd, M.K.1    French, A.D.2    Reilly, P.J.3
  • 15
    • 0000149351 scopus 로고
    • Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers
    • B. Hardy and A. Sarko, "Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers," J. Comput. Chem., vol. 14, no. 7, pp. 831-847, 1993.
    • (1993) J. Comput. Chem. , vol.14 , Issue.7 , pp. 831-847
    • Hardy, B.1    Sarko, A.2
  • 16
    • 84986522941 scopus 로고
    • A force field for monosaccharides and (1 → 4) linked polysaccharides
    • T. M. Glennon, Y. Zheng, S. M. le Grand, B. A. Shutzberg, and K. M. J. Merz, "A force field for monosaccharides and (1 → 4) linked polysaccharides." J. Comput. Chem., vol. 15, no. 9, pp. 1019-1040, 1994.
    • (1994) J. Comput. Chem. , vol.15 , Issue.9 , pp. 1019-1040
    • Glennon, T.M.1    Zheng, Y.2    Le Grand, S.M.3    Shutzberg, B.A.4    Merz, K.M.J.5
  • 17
    • 0001619856 scopus 로고    scopus 로고
    • Water Structure about the Dimer and Hexamer Repeat Units of Amylose from Molecular Dynamics Computer Simulations
    • DOI 10.1002/1096-987X(200103)22:4<445::AID-JCC1015>3.0.CO;2-P
    • K. J. Naidoo and M. Kuttel, "Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations," J. Comput. Chem., vol. 22, no. 4, pp. 445-456, 2001. (Pubitemid 33640783)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.4 , pp. 445-456
    • Naidoo, K.J.1    Kuttel, M.2
  • 18
    • 0035942932 scopus 로고    scopus 로고
    • Molecular dynamics and NMR study of the α(1→4) and α(1→6) glycosidic linkages: Maltose and isomaltose
    • R. B. Best, G. E. Jackson, and K. J. Naidoo, "Molecular dynamics and NMR study of the α(1→4) and α(1→6) glycosidic linkages: maltose and isomaltose," J. Phys. Chem. B, vol. 105, pp. 4742-4751, 2001.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 4742-4751
    • Best, R.B.1    Jackson, G.E.2    Naidoo, K.J.3
  • 19
    • 0035690998 scopus 로고    scopus 로고
    • Molecular dynamics simulation of neocarrabiose 2,4-bis(sulfate) and carrabiose 4,2-bis(sulfate) as building blocks of t-carrageenan in water
    • DOI 10.1246/bcsj.74.2269
    • K. Ueda, K. Iwama, and H. Nakayama, "Molecular dynamics simulation of neocarrabiose 2,4-bis(sulfate) and carrabiose 4,2-bis(sulfate) as building blocks of ι-carrageenan in water," Bull. Chem. Soc. Jpn., vol. 74, no. 12, pp. 2269-2277, 2001. (Pubitemid 34073787)
    • (2001) Bulletin of the Chemical Society of Japan , vol.74 , Issue.12 , pp. 2269-2277
    • Ueda, K.1    Iwama, K.2    Nakayama, H.3
  • 20
    • 1542285296 scopus 로고    scopus 로고
    • A hydration study of (1→4) and (1→6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR
    • F. Corzana, M. S. Motawia, C. H. D. Penhoat, S. Pèrez, S. M. Tschampel, R. J. Woods, and S. B. Engelsen, "A hydration study of (1→4) and (1→6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR," J. Comput. Chem., vol. 25, no. 4, pp. 573-586, 2004.
    • (2004) J. Comput. Chem. , vol.25 , Issue.4 , pp. 573-586
    • Corzana, F.1    Motawia, M.S.2    Penhoat, C.H.D.3    Pèrez, S.4    Tschampel, S.M.5    Woods, R.J.6    Engelsen, S.B.7
  • 21
    • 46049107338 scopus 로고    scopus 로고
    • Conformational flexibility of sulphur linked saccharides a possible key to their glycosidase inhibitor activity
    • G. A. Venter, R. P. Matthews, and K. J. Naidoo, "Conformational flexibility of sulphur linked saccharides a possible key to their glycosidase inhibitor activity," Molecular Simulation, vol. 34, no. 4, pp. 391-401, 2008.
    • (2008) Molecular Simulation , vol.34 , Issue.4 , pp. 391-401
    • Venter, G.A.1    Matthews, R.P.2    Naidoo, K.J.3
  • 23
  • 24
    • 24144451813 scopus 로고    scopus 로고
    • A new GROMOS force field for hexopyranose-based carbohydrates
    • R. D. Lins and P. H. Hünenberger, "A new GROMOS force field for hexopyranose-based carbohydrates," J. Comput. Chem., vol. 26, no. 13, pp. 1400-1412, 2005.
    • (2005) J. Comput. Chem. , vol.26 , Issue.13 , pp. 1400-1412
    • Lins, R.D.1    Hünenberger, P.H.2
  • 25
    • 0036771632 scopus 로고    scopus 로고
    • Carbohydrate solution simulations: Producing a force field with experimentally consistent primary alcohol rotational frequencies and populations
    • DOI 10.1002/jcc.10119
    • M. Kuttel, J. W. Brady, and K. J. Naidoo, "Carbohydrate solution simulations: Producing a force field with experimentally consistent hydroxyl rotational frequencies," J. Comput. Chem., vol. 23, no. 13, pp. 1236-1243, 2002. (Pubitemid 35017037)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.13 , pp. 1236-1243
    • Kuttel, M.1    Brady, J.W.2    Naidoo, K.J.3
  • 27
    • 66749083288 scopus 로고    scopus 로고
    • CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol
    • E. Hatcher, O. Guvench, and A. D. MacKerell, Jr., "CHARMM additive all-atom force field for acyclic polyalcohols, acyclic carbohydrates, and inositol," J. Chem. Theory Comput., vol. 5, no. 5, pp. 1315-1327, 2009.
    • (2009) J. Chem. Theory Comput. , vol.5 , Issue.5 , pp. 1315-1327
    • Hatcher, E.1    Guvench, O.2    MacKerell Jr., A.D.3
  • 28
    • 70349125512 scopus 로고    scopus 로고
    • CHARMM additive allatom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose
    • E. Hatcher, O. Guvench, and A. D. MacKerell, "CHARMM additive allatom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose," J. Phys. Chem. B., vol. 113, no. 37, pp. 12 466-12 476, 2009.
    • (2009) J. Phys. Chem. B. , vol.113 , Issue.37 , pp. 12466-12476
    • Hatcher, E.1    Guvench, O.2    MacKerell, A.D.3
  • 30
    • 35648984230 scopus 로고    scopus 로고
    • Incorporation of carbohydrates into macromolecular force fields: Development and validation
    • NMR spectroscopy and computer modeling of carbohydrates: recent advances, ser. J. F. G. Vliegenthart and R. J. Woods, Eds.
    • S. M. Tschampel, K. N. Kirschner, and R. J. Woods, "Incorporation of carbohydrates into macromolecular force fields: Development and validation,"in NMR spectroscopy and computer modeling of carbohydrates: recent advances, ser. ACS Symposium Series, J. F. G. Vliegenthart and R. J. Woods, Eds., vol. 930, 2006, pp. 235-257.
    • (2006) ACS Symposium Series , vol.930 , pp. 235-257
    • Tschampel, S.M.1    Kirschner, K.N.2    Woods, R.J.3
  • 31
    • 70349769322 scopus 로고    scopus 로고
    • Comparison of different force fields for the study of disaccharides
    • C. A. Stortz, G. P. Johnson, A. D. French, and G. I. Csonka, "Comparison of different force fields for the study of disaccharides," Carbohydr. Res., vol. 344, pp. 2217-2228, 2009.
    • (2009) Carbohydr. Res. , vol.344 , pp. 2217-2228
    • Stortz, C.A.1    Johnson, G.P.2    French, A.D.3    Csonka, G.I.4
  • 32
    • 84856360512 scopus 로고    scopus 로고
    • July. [Online]. Available
    • (2011, July). [Online]. Available: http://www.ks.uiuc.edu/Research/vmd/ plugins/psfgen/
    • (2011)
  • 33
    • 11844264892 scopus 로고    scopus 로고
    • Glycosidic linkage rotations determine amylose stretching mechanism
    • DOI 10.1021/ja047138s
    • M. Kuttel and K. J. Naidoo, "Glycosidic linkage rotations determine amylose stretching mechanism," J. Am. Chem. Soc., vol. 127, pp. 12-13, 2005. (Pubitemid 40094340)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.1 , pp. 12-13
    • Kuttel, M.1    Naidoo, K.J.2
  • 34
    • 13444283836 scopus 로고    scopus 로고
    • Carbohydrate Structure Suite (CSS): Analysis of carbohydrate 3D structures derived from the PDB
    • DOI 10.1093/nar/gki013
    • T. Lütteke, M. Frank, and C.-W. von der Lieth, "Carbohydrate structure suite (CSS): analysis of carbohydrate 3D structures derived from the PDB," Nucleic Acids Res., vol. 33, pp. D242-D246, 2005. (Pubitemid 40207870)
    • (2005) Nucleic Acids Research , vol.33 , Issue.DATABASE ISS.
    • Lutteke, T.1    Frank, M.2    Von Der, L.C.-W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.