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Lattice Centering and Coordination Number

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Related Experiment Video

Updated: Jan 21, 2026

Efficiently Recording the Eye-Hand Coordination to Incoordination Spectrum

Efficiently Recording the Eye-Hand Coordination to Incoordination Spectrum

Published on: March 21, 2019

Fast, efficient fragment-based coordinate generation for Open Babel.

Naruki Yoshikawa¹, Geoffrey R Hutchison²

¹Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

Journal of Cheminformatics

|August 3, 2019

Summary

This summary is machine-generated.

A new fragment-based method accelerates molecular structure prediction for cheminformatics. This open-source Open Babel implementation enhances speed and stereochemical accuracy, benefiting drug design and materials science.

Keywords:

Coordinate generation Fragments Molecular geometry

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Area of Science:

Computational chemistry
Cheminformatics
Molecular modeling

Background:

Accurate 3D molecular geometry prediction is vital for cheminformatics and molecular modeling.
Developing fast, accurate, and open-source tools is essential for reproducible research.

Purpose of the Study:

Introduce a novel fragment-based coordinate generation implementation for Open Babel.
Improve the speed and stereochemical accuracy of molecular structure prediction.

Main Methods:

Molecules are fragmented at rotatable bonds.
Fragment coordinates are generated using a library derived from crystallographic databases.
This approach determines multiple atom coordinates simultaneously.

Main Results:

The new implementation significantly accelerates coordinate prediction compared to previous methods.
It maintains or improves accuracy in bond lengths, angles, and dihedral torsions.
Enhanced stereochemical accuracy is achieved.

Conclusions:

The fragment-based approach offers a faster and more accurate method for 3D molecular structure prediction.
This open-source tool benefits cheminformatics research and applications like drug design and materials science.
The implementation integrates seamlessly with the Open Babel toolkit.