CMLSnap: Animated reaction mechanisms

G L  Holliday; John B. O. Mitchell; P  Murray-Rust

CMLSnap: Animated reaction mechanisms

G L Holliday, John B. O. Mitchell, P Murray-Rust

Research output: Contribution to journal › Article › peer-review

Abstract

Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions.

It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin.

Original language	English
Number of pages	6
Journal	Internet Journal of Chemistry
Volume	7
Issue number	4
Publication status	Published - 26 Oct 2004

Keywords

Reaction mechanisms
Animation
Enzyme reaction mechanisms
A BETA-LACTAMASES

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Cite this

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author = "Holliday, {G L} and Mitchell, {John B. O.} and P Murray-Rust",

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AU - Holliday, G L

AU - Mitchell, John B. O.

AU - Murray-Rust, P

N1 - The authors thank the EPSRC for financial support of this project and Unilever for their support of the Centre for Molecular Science Informatics.

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N2 - Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions. It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin.

AB - Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions. It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin.

KW - Reaction mechanisms

KW - Animation

KW - Enzyme reaction mechanisms

KW - A BETA-LACTAMASES

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VL - 7

JO - Internet Journal of Chemistry

JF - Internet Journal of Chemistry

IS - 4

ER -

CMLSnap: Animated reaction mechanisms

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Keywords

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