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

Automated refinement of protein models.

V S Lamzin1, K S Wilson

  • 1European Molecular Biology Laboratory, Hamburg, Germany.

Acta Crystallographica. Section D, Biological Crystallography
|January 1, 1993
PubMed
Summary

An automated refinement procedure (ARP) offers a faster method for protein model building, comparable to traditional techniques. This automated approach yields similar results to conventional refinement for high-resolution protein data.

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

[Scaffold hopping computational approach for searching novel β-lactamase inhibitors].

Biomeditsinskaia khimiia·2019
Same author

An evaluation of the implementation of a parent-led, games-based physical activity intervention: the Active Play at Home quasi-randomized trial.

Health education research·2018
Same author

Correction: Analysis of unstable modes distinguishes mathematical models of flagellar motion.

Journal of the Royal Society, Interface·2017
Same author

Novel non-β-lactam inhibitor of β-lactamase TEM-171 based on acylated phenoxyaniline.

Biochimie·2016
Same author

Early-life glucocorticoids programme behaviour and metabolism in adulthood in zebrafish.

The Journal of endocrinology·2016
Same author

Tomography of a Cryo-immobilized Yeast Cell Using Ptychographic Coherent X-Ray Diffractive Imaging.

Biophysical journal·2015

Area of Science:

  • Structural biology
  • Computational biology
  • X-ray crystallography

Background:

  • Protein model refinement is crucial for accurate structural determination.
  • Conventional methods like least-squares minimization are computationally intensive.
  • Automated approaches can potentially accelerate the refinement process.

Purpose of the Study:

  • To introduce and evaluate an automated refinement procedure (ARP) for protein models.
  • To assess the convergence properties and efficiency of ARP.
  • To compare ARP's performance against conventional refinement techniques.

Main Methods:

  • Development of an automated refinement procedure (ARP).
  • Application of ARP to three protein datasets.
  • Comparison of ARP-refined models with those from conventional least-squares refinement and rebuilding with FRODO.

Main Results:

  • ARP demonstrated comparable results to conventional methods for two out of three proteins at high resolution (2.0 Å or better).
  • ARP achieved refinement approximately ten times faster than conventional methods in real time.
  • For a third protein at 2.4 Å resolution, ARP showed improvement, particularly in the density map, though less powerful than at higher resolutions.

Conclusions:

  • ARP is an efficient automated method for protein model refinement, especially with high-quality, high-resolution data.
  • The procedure requires a good starting model and high-resolution data for optimal performance.
  • ARP offers a significant speed advantage over traditional refinement techniques.

Related Experiment Videos