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Harbison AM, Brosnan LP, Fenlon K, Fadda E. Sequence-to-structure dependence of isolated IgG Fc complex biantennary N -glycans: a molecular dynamics study. Glycobiology 2019;29:94-103. [DOI: 10.1093/glycob/cwy097] [Cited by in Crossref: 26] [Cited by in F6Publishing: 20] [Article Influence: 6.5] [Reference Citation Analysis]
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Roy R, Jonniya NA, Sk MF, Kar P. Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations. Front Mol Biosci 2022;9:852895. [DOI: 10.3389/fmolb.2022.852895] [Reference Citation Analysis]
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Alibay I, Bryce RA. Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. J Chem Inf Model 2019;59:4729-41. [PMID: 31609614 DOI: 10.1021/acs.jcim.9b00529] [Cited by in Crossref: 9] [Cited by in F6Publishing: 7] [Article Influence: 3.0] [Reference Citation Analysis]
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Roy R, Poddar S, Sk MF, Kar P. Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations. J Biomol Struct Dyn 2022;:1-16. [PMID: 35262462 DOI: 10.1080/07391102.2022.2047109] [Reference Citation Analysis]
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Yamasaki K, Kubota T, Yamasaki T, Nagashima I, Shimizu H, Terada R, Nishigami H, Kang J, Tateno M, Tateno H. Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL). Glycobiology 2019;29:576-87. [DOI: 10.1093/glycob/cwz025] [Cited by in Crossref: 4] [Cited by in F6Publishing: 2] [Article Influence: 1.3] [Reference Citation Analysis]
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Borenstein-Katz A, Warszawski S, Amon R, Eilon M, Cohen-Dvashi H, Leviatan Ben-Arye S, Tasnima N, Yu H, Chen X, Padler-Karavani V, Fleishman SJ, Diskin R. Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies. J Mol Biol 2021;433:167099. [PMID: 34119488 DOI: 10.1016/j.jmb.2021.167099] [Reference Citation Analysis]
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Roy R, Ghosh B, Kar P. Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics. ACS Omega 2020;5:3932-42. [PMID: 32149220 DOI: 10.1021/acsomega.9b03398] [Cited by in Crossref: 23] [Cited by in F6Publishing: 20] [Article Influence: 11.5] [Reference Citation Analysis]
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Whitmore EK, Martin D, Guvench O. Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics. Int J Mol Sci 2020;21:E7699. [PMID: 33080973 DOI: 10.3390/ijms21207699] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 2.0] [Reference Citation Analysis]
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020;21:E7702. [PMID: 33081008 DOI: 10.3390/ijms21207702] [Cited by in Crossref: 4] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
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Fogarty CA, Harbison AM, Dugdale AR, Fadda E. How and why plants and human N-glycans are different: Insight from molecular dynamics into the "glycoblocks" architecture of complex carbohydrates. Beilstein J Org Chem 2020;16:2046-56. [PMID: 32874351 DOI: 10.3762/bjoc.16.171] [Cited by in Crossref: 4] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
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Roy R, Jonniya NA, Kar P. Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study. J Phys Chem B 2022. [PMID: 35594147 DOI: 10.1021/acs.jpcb.2c01807] [Reference Citation Analysis]
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Lepsik M, Sommer R, Kuhaudomlarp S, Lelimousin M, Paci E, Varrot A, Titz A, Imberty A. Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study. Eur J Med Chem 2019;177:212-20. [PMID: 31146126 DOI: 10.1016/j.ejmech.2019.05.049] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 0.7] [Reference Citation Analysis]
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Suzuki T, Yanaka S, Watanabe T, Yan G, Satoh T, Yagi H, Yamaguchi T, Kato K. Remodeling of the Oligosaccharide Conformational Space in the Prebound State To Improve Lectin-Binding Affinity. Biochemistry 2020;59:3180-5. [PMID: 31553574 DOI: 10.1021/acs.biochem.9b00594] [Cited by in Crossref: 3] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
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Hahn DF, Hünenberger PH. Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme. J Chem Theory Comput 2019;15:2392-419. [PMID: 30821973 DOI: 10.1021/acs.jctc.8b00782] [Cited by in Crossref: 13] [Cited by in F6Publishing: 10] [Article Influence: 4.3] [Reference Citation Analysis]
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