Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Slow-cooling protocols for crystallographic refinement by simulated annealing.

A T Brünger1, A Krukowski, J W Erickson

  • 1Howard Hughes Medical Institute, New Haven, CT.

Acta Crystallographica. Section A, Foundations of Crystallography
|July 1, 1990
PubMed
Summary

This study introduces an improved simulated annealing protocol for crystallographic refinement using slow cooling. This new method achieves lower R factors and better structural geometry in protein refinement compared to existing protocols.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A smooth and differentiable bulk-solvent model for macromolecular diffraction.

Acta crystallographica. Section D, Biological crystallography·2010
Same author

Climate change and the integrity of science.

Science (New York, N.Y.)·2010
Same author

Highly specific interactions between botulinum neurotoxins and synaptic vesicle proteins.

Cellular and molecular life sciences : CMLS·2008
Same author

Structural characterization of the intramolecular interaction between the SH3 and guanylate kinase domains of PSD-95.

Molecular cell·2002
Same author

Sex and the neighboring cell.

Developmental cell·2001
Same author

Structure of proteins involved in synaptic vesicle fusion in neurons.

Annual review of biophysics and biomolecular structure·2001

Area of Science:

  • Structural biology
  • Computational chemistry
  • Biophysics

Background:

  • Crystallographic refinement is crucial for determining accurate 3D structures of molecules.
  • Simulated annealing is a computational technique used to optimize structures.
  • Existing simulated annealing protocols may not always yield optimal results.

Purpose of the Study:

  • To present an improved protocol for crystallographic refinement using simulated annealing.
  • To investigate the effectiveness of a slow-cooling strategy within simulated annealing.
  • To compare the new protocol against previously published methods.

Main Methods:

  • Development of a slow-cooling protocol for simulated annealing, starting at high temperatures.
  • Application of the protocol to refine the structures of aspartate aminotransferase and porcine pepsin.

Related Experiment Videos

  • Systematic study of parameters influencing the slow-cooling protocol, including temperature control, weighting, cooling rate, and heating duration.
  • Analysis of potential energy fluctuations to understand system dynamics.

    • Main Results:

    • The slow-cooling protocol consistently produced lower R factors compared to other published protocols.
    • The improved protocol resulted in better crystallographic geometry.
    • Analysis revealed potential energy fluctuations interpreted as localized conformational changes, not global order changes.

    Conclusions:

    • The presented slow-cooling simulated annealing protocol offers superior performance for crystallographic refinement.
    • This method enhances structural accuracy and geometric quality in molecular modeling.
    • The findings contribute to more precise structural determination in fields like structural biology and drug discovery.