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Updated: Jun 19, 2026

Three-Dimensional Mapping of the Rotation of Interactive Virtual Objects with Eye-Tracking Data
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Computation of 3D queries for ROCS based virtual screens.

Gregory J Tawa1, J Christian Baber, Christine Humblet

  • 1Chemical Sciences, Wyeth Research, Princeton, NJ, USA. tawag@wyeth.com

Journal of Computer-Aided Molecular Design
|October 13, 2009
PubMed
Summary

Using CORAL (Conformational analysis, ROCS Alignment) for virtual screening improves hit list enrichment compared to standard minimum energy structures. This method optimizes conformation selection for better results in ROCS alignment.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • cheminformatics

Background:

  • Rapid Overlay of Chemical Structures (ROCS) is a key method for 3D ligand-based virtual screening.
  • ROCS alignment typically uses a single minimum energy conformation for query molecules.
  • The effectiveness of using alternative conformations for ROCS screening remains an area for investigation.

Purpose of the Study:

  • To introduce and evaluate CORAL (Conformational analysis, ROCS Alignment), a novel methodology for optimizing conformation selection in ROCS screening.
  • To determine if using CORAL-selected conformations yields better enrichment in virtual screening compared to minimum energy conformations.

Main Methods:

  • CORAL identifies optimal ROCS screening conformations by clustering molecular conformers based on pairwise ROCS combo scores.
  • The best representative conformation within each cluster exhibits the highest average overlap with other conformers.
  • Virtual screening experiments were conducted using the 40 DUD (Directory of Useful Decoys) datasets, comparing CORAL and minimum energy queries.

Main Results:

  • Virtual screening experiments demonstrated that CORAL-derived queries achieved higher Area Under the ROC Curve (AUC) values on average than minimum energy queries.
  • This indicates superior recognition capability and enrichment performance when using CORAL-optimized conformations.
  • The findings validate that non-minimum energy conformations can enhance ROCS screening efficacy.

Conclusions:

  • CORAL analysis provides a valuable enhancement to virtual screening workflows that utilize ROCS alignment.
  • Employing CORAL-selected conformations can lead to more effective 3D ligand-based virtual screening.
  • This methodology offers a pathway to improve hit identification rates in drug discovery pipelines.