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e-molecular shapes and properties.

A J M Carpy1, N Marchand-Geneste

  • 1Laboratoire de Physico- et Toxico-Chimie des Systèmes Naturels, UMR 5472 CNRS, Université de Bordeaux 1, 351, Cours de la Libération 33405, Talence cedex, France. a.carpy@lptc.u-bordeaux1.fr

SAR and QSAR in Environmental Research
|February 5, 2004
PubMed
Summary

Advances in computer technology enable detailed molecular surface analysis for drug design and proteomics. This review covers freely available online resources for computing and visualizing molecular and buried surfaces and their shape properties.

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Structural e-bioinformatics and drug design.

SAR and QSAR in environmental research·2006

Area of Science:

  • Computational chemistry and structural biology
  • Molecular modeling and bioinformatics

Background:

  • Computer technology advancements have increased the importance of shape analysis.
  • Molecular surfaces and buried surfaces are crucial in understanding molecular interactions.

Purpose of the Study:

  • To review freely available internet resources for shape analysis in drug design and proteomics.
  • To highlight the computational and visualization capabilities for molecular surfaces.

Main Methods:

  • Review of online resources and computational tools.
  • Description of methods for computing various molecular surfaces (e.g., van der Waals, solvent accessible, solvent excluded, polar surface area, electron density).
  • Discussion of buried surface computations (e.g., gap, cleft, cavity).

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Main Results:

  • Identification of accessible internet resources for academic use.
  • Demonstration of the ease of computing and visualizing molecular and buried surfaces.
  • Overview of shape properties analysis for these surfaces.

Conclusions:

  • Freely available online resources facilitate advanced shape analysis in drug design and proteomics.
  • These tools are valuable for researchers in computational chemistry and structural biology.
  • The accessibility of these resources promotes wider application of shape analysis techniques.