Journal of Computer-Aided Molecular Design

, Volume 20, Issue 10, pp 647–671

PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results

  • Steven L. Dixon
  • Alexander M. Smondyrev
  • Eric H. Knoll
  • Shashidhar N. Rao
  • David E. Shaw
  • Richard A. Friesner
Original Paper

DOI: 10.1007/s10822-006-9087-6

Cite this article as:
Dixon, S.L., Smondyrev, A.M., Knoll, E.H. et al. J Comput Aided Mol Des (2006) 20: 647. doi:10.1007/s10822-006-9087-6

Summary

We introduce PHASE, a highly flexible system for common pharmacophore identification and assessment, 3D QSAR model development, and 3D database creation and searching. The primary workflows and tasks supported by PHASE are described, and details of the underlying scientific methodologies are provided. Using results from previously published investigations, PHASE is compared directly to other ligand-based software for its ability to identify target pharmacophores, rationalize structure-activity data, and predict activities of external compounds.

Keywords

Pharmacophore perception3D QSAR3D databasesLigand-based design

Copyright information

© Springer Science+Business Media, LLC 2006

Authors and Affiliations

  • Steven L. Dixon
    • 1
  • Alexander M. Smondyrev
    • 1
  • Eric H. Knoll
    • 1
    • 2
  • Shashidhar N. Rao
    • 1
  • David E. Shaw
    • 1
    • 3
  • Richard A. Friesner
    • 1
    • 2
  1. 1.Schrödinger, Inc.New YorkUSA
  2. 2.Department of ChemistryColumbia UniversityNew YorkUSA
  3. 3.D E Shaw & CoNew YorkUSA