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Unconventional 2D shape similarity method affords comparable enrichment as a 3D shape method in virtual screening

Jerry Osagie Ebalunode1, Weifan Zheng

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

Journal of Chemical Information and Modeling
|June 2, 2009
PubMed
Summary

A novel 2D shape similarity method offers a computationally efficient alternative to 3D methods like ROCS for virtual screening. This approach simplifies calculations by comparing 2D chemical depictions, proving effective in drug discovery.

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • 3D molecular shape similarity is crucial for virtual screening and scaffold hopping in drug discovery.
  • ROCS (Rapid Overlay of Chemical Structures) is an efficient 3D similarity tool, but searching large multiconformer databases is challenging.
  • Computational efficiency is a key consideration for large-scale virtual screening.

Purpose of the Study:

  • To explore an alternative shape similarity approach that bypasses the need for multiconformer calculations.
  • To develop a computationally efficient method for large-scale virtual screening.
  • To assess the performance of a 2D shape similarity method against established 3D methods.

Main Methods:

  • Generated 2D chemical depictions for query and database molecules using a 2D depiction program.
  • Developed a 2D shape comparison program utilizing the OESHAPE Toolkit.
  • Quantified molecular shape similarity by comparing 2D chemical drawings.
  • Evaluated the method's performance in virtual screening experiments.

Main Results:

  • The 2D shape similarity method demonstrated fair performance in virtual screening experiments.
  • The 2D method showed comparable results to the 3D Shape method ROCS.
  • A significant advantage of the 2D method is its enhanced computational efficiency.

Conclusions:

  • A 2D shape similarity approach provides a viable and computationally efficient alternative for virtual screening.
  • This method simplifies the process by avoiding complex 3D multiconformer calculations.
  • The findings suggest potential for accelerating drug discovery and chemical genomics research.