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 Concept Videos

You might also read

Related Articles

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

Sort by
Same author

<i>OCA2</i> common variant NM_000275.3:c.574-19A>G affects splicing and is pathogenic.

Molecular genetics and metabolism reports·2026
Same author

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same author

DirectASRM: Uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.

Bioinformatics (Oxford, England)·2026
Same author

AlphaFold reveals how pathogenic <i>Leptospira</i> use cross-kingdom thiol-disulfide exchange to evade the complement membrane attack complex.

mBio·2026
Same author

An AI-Ready Phosphorylation Meta-Analysis for <i>Saccharomyces cerevisiae</i>.

Journal of proteome research·2026
Same author

The promise of AlphaFold for gene structure annotation.

Nucleic acids research·2026
Same journal

Structural insights into the synthesis of FMN in prokaryotic organisms.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Native sulfur/chlorine SAD phasing for serial femtosecond crystallography.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Serial crystallographic analysis of protein isomorphous replacement data from a mixture of native and derivative microcrystals.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

The first crystal structure of the peptidase domain of the U32 peptidase family.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.

Acta crystallographica. Section D, Biological crystallography·2015
Same journal

Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.

Acta crystallographica. Section D, Biological crystallography·2015
See all related articles

Related Experiment Video

Updated: Jun 27, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
11:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Molecular replacement using ab initio polyalanine models generated with ROSETTA.

Daniel J Rigden1, Ronan M Keegan, Martyn D Winn

  • 1School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England. rigden@liv.ac.uk

Acta Crystallographica. Section D, Biological Crystallography
|November 20, 2008
PubMed
Summary
This summary is machine-generated.

Generating ab initio models using ROSETTA for protein structure determination via molecular replacement shows promise. This approach, using modest computational resources, can yield correct solutions for solving protein structures from diffraction data.

More Related Videos

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
10:27

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Related Experiment Videos

Last Updated: Jun 27, 2026

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
11:27

X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
10:27

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • The molecular replacement method is crucial for solving protein structures from experimental diffraction data.
  • A suitable search model, typically from a solved structure or homology modeling, is essential for molecular replacement.
  • Recent work has shown success using ab initio models generated by ROSETTA for molecular replacement.

Purpose of the Study:

  • To report additional test cases of ab initio models generated by ROSETTA for molecular replacement.
  • To investigate the factors influencing the success of ab initio models in protein structure solution.
  • To provide a comparison of successful and unsuccessful cases.

Main Methods:

  • Generation of ab initio models using the ROSETTA software.
  • Application of these ab initio models in the molecular replacement method.
  • Analysis of successful and unsuccessful molecular replacement solutions.

Main Results:

  • Demonstration of successful molecular replacement solutions using ab initio models generated with modest computational resources.
  • Identification of specific test cases where this approach is effective.
  • Reporting of unsuccessful cases to delineate limitations.

Conclusions:

  • Ab initio models generated by ROSETTA can be successfully employed in molecular replacement for protein structure determination.
  • The success of this method depends on various factors that influence the quality of the ab initio model and its suitability for molecular replacement.
  • This approach offers a viable alternative for solving protein structures, particularly when suitable search models are unavailable.