Conformational Analysis of Carbohydrates – A Historical Overview

Frank, Martin

doi:10.1002/9780470029619.ch18

Cited by 3 publications

(3 citation statements)

References 204 publications

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“…To date, the following theoretical models and methods are applied for in silico design of carbohydrate three-dimensional structure [ 112 , 113 , 114 , 115 , 116 ]: Molecular mechanics (MM) and molecular dynamics (MD) calculations [ 117 ]; Monte Carlo simulations [ 118 , 119 ]; Semi-empirical methods [ 120 , 121 , 122 , 123 ]; Ab initio simulations based on density functional theory (DFT) [ 124 , 125 , 126 , 127 , 128 ]; Hybrid QM/MM and QM/QM and ONIOM (“our own N-layered integrated molecular orbital and molecular mechanics”) approaches [ 129 , 130 , 131 , 132 , 133 , 134 ]. …”

Section: Carbohydrate 3d Structure Modelingmentioning

confidence: 99%

“…Molecular dynamics methods have achieved broad scope of application in terms of reasonable computer resource consumption. They fulfill advantageous compromise between calculation accuracy and performance, when applied to glycan molecules and their structural complexity (variety of known monomeric elements, presence of ionogenic groups), high bridge flexibility and stereo-electronic effects [ 112 , 113 , 136 , 137 ].…”

Section: Carbohydrate 3d Structure Modelingmentioning

confidence: 99%

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Three-Dimensional Structures of Carbohydrates and Where to Find Them

Scherbinina

Toukach

2020

IJMS

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Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

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Section: Carbohydrate 3d Structure Modelingmentioning

confidence: 99%

Section: Carbohydrate 3d Structure Modelingmentioning

confidence: 99%

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Scherbinina

Toukach

2020

IJMS

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“…NMR spectroscopy, taken in conjunction with computational techniques and fitting procedures, can provide a near-complete picture of a molecule's solution geometry. [1][2][3][4][5] A particularly useful tool to determine a molecule's geometry is the Karplus relation between a coupling constant and dihedral angle of the coupled atoms, based originally on the Fermi Contact contribution in the early theories of NMR coupling phenomena. [6][7][8] The Karplus equation can describe quantitatively the correlation of experimental coupling constant to the dihedral angle between the coupled nuclei and has been used very successfully to derive molecular structures.…”

Section: Introductionmentioning

confidence: 99%

Development of a Karplus equation for 3JCOCH in ester-functionalized glucopyranoses and methylglucuronate.

Hackbusch¹,

Watson²,

Franz³

2017

Arkivoc

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Empirical Karplus equations are very useful in the conformational analysis of flexible molecules, especially with regards to carbohydrates. The C(sp 2 )OCH dihedral angle of ester-functionalized carbohydrates, however, is not well described by widely used Karplus equations for COCH dihedral angles, because they are based on C(sp 3 )OCH data. Herein, we propose a three parameter Karplus equation of the form 3 JCOCH = 5.18 cos 2 (*) -1.42 cos(*) + 1.05 on the basis of quantum mechanics computations for 6-O-acetyl-α/ß-D-glucopyranose. The equation gives satisfactory agreement between experimentally determined 3 JCH values and those back calculated from MD simulations using the GLYCAM06 forcefield for a set of acetylated glucoses and methyl glucuronate.

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Bioinformatics and molecular modeling in glycobiology

Frank

Schloissnig

2010

Cell. Mol. Life Sci.

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The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed.

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Conformational Analysis of Carbohydrates – A Historical Overview

Cited by 3 publications

References 204 publications

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Development of a Karplus equation for 3JCOCH in ester-functionalized glucopyranoses and methylglucuronate.

Bioinformatics and molecular modeling in glycobiology

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