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Related Concept Videos

Molecular Shapes01:18

Molecular Shapes

62.8K
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...
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Molecular Models02:00

Molecular Models

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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.
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Newman Projections02:06

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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...
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Fischer Projections02:18

Fischer Projections

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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...
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VSEPR Theory02:37

VSEPR Theory

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Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...
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VSEPR Theory and the Basic Shapes02:52

VSEPR Theory and the Basic Shapes

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Overview of VSEPR Theory
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Interactive Molecular Model Assembly with 3D Printing
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A Simple Representation of Three-Dimensional Molecular Structure.

Seth D Axen1, Xi-Ping Huang2,3, Elena L Cáceres1,4

  • 1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco , 675 Nelson Rising Lane NS 416A, San Francisco, California 94143, United States.

Journal of Medicinal Chemistry
|July 22, 2017
PubMed
Summary
This summary is machine-generated.

A new 3D molecular fingerprint, extended three-dimensional fingerprint (E3FP), improves drug-to-target predictions. E3FP enhances similarity searching and identifies novel drug-target interactions missed by 2D methods.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Machine learning models predict drug-target interactions using 2D molecular structures.
  • Incorporating 3D molecular information is hypothesized to improve prediction accuracy.

Purpose of the Study:

  • To develop a rapid, alignment-invariant 3D molecular representation called extended three-dimensional fingerprint (E3FP).
  • To evaluate E3FP's performance in predicting drug-to-target relationships compared to existing 2D methods.

Main Methods:

  • Applied the extended connectivity fingerprint (ECFP) logic to create the 3D extended three-dimensional fingerprint (E3FP).
  • Integrated E3FP with the Similarity Ensemble Approach (SEA) for drug-target prediction.
  • Validated predictions experimentally.

Main Results:

  • E3FP combined with SEA showed improved precision-recall performance over SEA with ECFP on the ChEMBL20 dataset.
  • Identified molecular classes where E3FP outperforms ECFP in predicting bioactivity similarity.
  • Discovered novel drug-to-target binding predictions not accessible by 2D fingerprints, with three confirmed experimentally.

Conclusions:

  • The extended three-dimensional fingerprint (E3FP) is an effective 3D molecular representation for drug-target interaction prediction.
  • E3FP enhances similarity searching and enables the discovery of novel drug-target relationships.
  • Experimental validation confirms the utility of E3FP-derived predictions.