Predicting Carbohydrate 3D Structures Using Theoretical Methods

Frank, Martin

doi:10.1002/9780470029619.ch19

Cited by 3 publications

(2 citation statements)

References 134 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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Conformational Analysis of Oligosaccharides and Polysaccharides Using Molecular Dynamics Simulations

Frank

2015

Methods in Molecular Biology

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Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

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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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Predicting Carbohydrate 3D Structures Using Theoretical Methods

Cited by 3 publications

References 134 publications

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Conformational Analysis of Oligosaccharides and Polysaccharides Using Molecular Dynamics Simulations

Bioinformatics and molecular modeling in glycobiology

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