Chapter

Chapter 18.10 PrimeX and the Schrödinger computational chemistry suite of programs

Crystallography of biological macromolecules

Second Online Edition (2012)

Part 18. Refinement

  1. J. A. Bell1,
  2. Y. Cao1,
  3. J. R. Gunn1,
  4. T. Day1,
  5. E. Gallicchio2,
  6. Z. Zhou1,
  7. R. Levy2,
  8. R. Farid1

Published Online: 14 APR 2012

DOI: 10.1107/97809553602060000864

International Tables for Crystallography

International Tables for Crystallography

How to Cite

Bell, J. A., Cao, Y., Gunn, J. R., Day, T., Gallicchio, E., Zhou, Z., Levy, R. and Farid, R. 2012. PrimeX and the Schrödinger computational chemistry suite of programs. International Tables for Crystallography. F:18:18.10:534–538.

Author Information

  1. 1

    Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA

  2. 2

    BioMaPS Institute for Quantitative Biology, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA

Publication History

  1. Published Online: 14 APR 2012

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Abstract

PrimeX is a new X‐ray crystal structure refinement program for biological macromolecules from Schrödinger, Inc. It produces an all‐atom model at moderate resolution that is in excellent agreement with the diffraction data and that is also suitable for immediate use in computational chemistry applications. The program features maximum‐likelihood reciprocal‐space minimization, simulated‐annealing refinement, ligand placement, loop building and side‐chain placement. PrimeX is integrated with the powerful molecular‐graphics program Maestro, which provides an easy‐to‐use graphical interface. Command‐line access to PrimeX tools provides for their scripting into complex workflows. Additional information about these features and the methods used therein are presented.

Keywords:

  • PrimeX;
  • Glide;
  • Prime;
  • Maestro;
  • real‐space minimization;
  • reciprocal‐space minimization;
  • simulated annealing;
  • side‐chain placement