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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...
Drug Discovery: Overview01:26

Drug Discovery: Overview

Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
Molecular Shape and Polarity03:37

Molecular Shape and Polarity

Dipole Moment of a Molecule
Structure-Activity Relationships and Drug Design01:28

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence its...
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.
VSEPR Theory and the Basic Shapes02:52

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Related Experiment Video

Updated: Jun 14, 2026

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

Molecular shape technologies in drug discovery: methods and applications.

Jerry O Ebalunode1, Weifan Zheng

  • 1Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC 27707, USA.

Current Topics in Medicinal Chemistry
|March 27, 2010
PubMed
Summary

Molecular shape comparison is key for drug discovery. Recent advances in computational tools now enable efficient and widespread use of shape-matching technologies for identifying new drug candidates.

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Last Updated: Jun 14, 2026

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Area of Science:

  • Computational chemistry
  • Medicinal chemistry
  • Drug discovery

Background:

  • Molecular recognition between drugs and biological receptors is crucial.
  • Historically, computational drug discovery utilized the principle that similar 3D molecular shapes often correlate with similar biological activity.
  • Early shape-matching algorithms were limited by computational inefficiency and lack of accessible software.

Purpose of the Study:

  • To summarize well-known molecular shape-matching algorithms used in drug discovery.
  • To describe the computational principles behind superposition-based and superposition-free methods.
  • To highlight recent validation studies and practical applications of shape technologies.

Main Methods:

  • Description of superposition-based methods: ROCS (Rapid Overlay of Compound Structures), SQ, and CatShape.
  • Description of superposition-free methods: shape signatures algorithm and USR (Ultrafast Shape Recognition).
  • Review of validation studies and practical applications of these shape-matching technologies.

Main Results:

  • Recent developments have led to fast and accurate shape comparison tools.
  • These advancements have facilitated the widespread adoption of ligand-based and receptor-based shape-matching in drug discovery.
  • Molecular shape technologies are becoming increasingly accessible due to affordable computational resources and software.

Conclusions:

  • Anticipation of broader use of molecular shape technologies in future drug discovery.
  • Molecular shape technologies are particularly valuable for chemogenomics research, enabling large-scale associations between small molecules and protein targets.
  • Combined with pharmacophore constraints, shape technologies offer efficient and effective approaches for drug discovery and chemical genomics.