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Related Concept Videos

Molecular Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Molecular Shape and Polarity03:37

Molecular Shape and Polarity

Dipole Moment of a Molecule

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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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3DMolNavi: a web-based retrieval and navigation tool for flexible molecular shape comparison.

Yu-Shen Liu1, Meng Wang, Jean-Claude Paul

  • 1School of Software, Tsinghua University, Beijing 100084, China. liuyushen@tsinghua.edu.cn

BMC Bioinformatics
|May 16, 2012
PubMed
Summary

This study introduces 3DMolNavi, a tool for comparing flexible molecule shapes. It improves data retrieval and navigation for users seeking similar molecules.

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Area of Science:

  • Computational chemistry
  • Structural biology
  • Bioinformatics

Background:

  • Flexible molecules undergo shape changes crucial for function, but rigid comparisons yield inaccurate similarity measures.
  • Existing methods lack effective retrieval and navigation for flexible molecular shape comparison.

Purpose of the Study:

  • To develop a web-based tool, 3DMolNavi, for flexible molecular shape comparison.
  • To enhance data retrieval and user navigation for flexible molecules.

Main Methods:

  • Utilizes histogram of Inner Distance Shape Signature (IDSS) for rapid retrieval of similar molecules.
  • Employs dimensionality reduction for navigating retrieved results in 2D and 3D spaces.
  • Tested on the Database of Macromolecular Movements (MolMovDB) and CATH.

Main Results:

  • 3DMolNavi demonstrates good performance and retrieval accuracy for diverse flexible molecules.
  • Achieves effective flexible molecular shape comparison and navigation.

Conclusions:

  • 3DMolNavi integrates retrieval and navigation for flexible molecular shape comparison, enhancing user interaction.
  • The tool offers advantages over existing software for flexible molecule analysis.
  • Accessible at https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html.