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Related Concept Videos

Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
Chemistry of Carbohydrates03:25

Chemistry of Carbohydrates

Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...
Chemistry of Carbohydrates03:25

Chemistry of Carbohydrates

Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...
Chemistry of Carbohydrates03:25

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Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...
Predicting Molecular Geometry02:27

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Conformations of Cyclohexane

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The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...

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Updated: Jun 14, 2026

Automated Modular High Throughput Exopolysaccharide Screening Platform Coupled with Highly Sensitive Carbohydrate Fingerprint Analysis
12:02

Automated Modular High Throughput Exopolysaccharide Screening Platform Coupled with Highly Sensitive Carbohydrate Fingerprint Analysis

Published on: April 11, 2016

Shape: automatic conformation prediction of carbohydrates using a genetic algorithm.

Jimmy Rosen1, Laurence Miguet, Serge Pérez

  • 1Bio Organic Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands. jimmy.rosen@gmail.com.

Journal of Cheminformatics
|March 20, 2010
PubMed
Summary

Shape software simplifies carbohydrate 3D structure prediction for researchers. This automated tool provides accurate conformation predictions on standard hardware, making complex molecular modeling accessible.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Automated Modular High Throughput Exopolysaccharide Screening Platform Coupled with Highly Sensitive Carbohydrate Fingerprint Analysis
12:02

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Published on: April 11, 2016

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Computational chemistry
  • Structural biology
  • Carbohydrate chemistry

Background:

  • Experimental determination of complex carbohydrate 3D structures is challenging.
  • Molecular modeling and computational conformation prediction are essential but resource-intensive.
  • Existing modeling tools often require specialized training and significant computing power.

Purpose of the Study:

  • To develop user-friendly software for automated carbohydrate conformation prediction.
  • To enhance the accessibility of molecular modeling for chemists and biologists.
  • To improve the efficiency of 3D structure studies for carbohydrates.

Main Methods:

  • Development of the Shape software package.
  • Implementation of a genetic algorithm for efficient conformation searching.
  • Creation of a simple user interface for automated modeling.

Main Results:

  • Shape successfully predicts conformations for carbohydrates up to several hundred atoms on common hardware.
  • The software demonstrates high performance in predicting over 400 bioactive oligosaccharides.
  • Results favorably compare with existing carbohydrate conformation prediction studies.

Conclusions:

  • Shape provides fully automated conformation prediction accessible to users without extensive modeling expertise.
  • The software performs well on standard computers and can be scaled to computer clusters.
  • Default settings yield accurate predictions consistent with experimental data and prior studies.