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

ARP/wARP's model-building algorithms. I. The main chain.

Richard J Morris1, Anastassis Perrakis, Victor S Lamzin

  • 1EMBL Hamburg c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Acta Crystallographica. Section D, Biological Crystallography
|May 31, 2002
PubMed
Summary
This summary is machine-generated.

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 P-type pentatricopeptide repeat-containing protein interacts with the Japanese soil-borne wheat mosaic virus movement protein and modulates susceptibility to infection.

The Journal of general virology·2026
Same author

A comprehensive UK crop yield dataset incorporating satellite, weather, and soil type information.

Scientific data·2026
Same author

Natural variation in Arabidopsis uncouples leaf and flower development and reveals massive transcriptomic heterochrony.

Journal of experimental botany·2026
Same author

Halogen bonds between ligands and proteins: Can we use them in validation?

Protein science : a publication of the Protein Society·2025
Same author

Evolving Patterns of Self-Efficacy for Clinical Tasks Among Speech-Language Pathology Graduate Students.

American journal of speech-language pathology·2025
Same author

DSSP 4: FAIR annotation of protein secondary structure.

Protein science : a publication of the Protein Society·2025
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

This study presents algorithms for automatic model building in the ARP/wARP software. It details how to efficiently find Calpha atoms using integer programming and graph-search methods for protein structure determination.

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Automatic model building is crucial for determining protein structures.
  • The ARP/wARP software suite is widely used in structural biology.
  • Efficient algorithms are needed to handle the complexity of atomic models.

Purpose of the Study:

  • To present the algorithms behind the automatic model-building functionality of the ARP/wARP software.
  • To formulate the problem of finding Calpha atoms as a constrained integer programming problem.
  • To introduce efficient graph-search algorithms for solving this problem.

Main Methods:

  • Formulation of Calpha atom identification as a constrained integer programming problem.
  • Development of a density-weighted score for matching observed and expected chain conformations.

Related Experiment Videos

  • Implementation of graph-search algorithms for efficient solution finding.

    • Main Results:

    • The presented algorithms enable efficient automatic model building.
    • The integer programming formulation effectively addresses the Calpha atom identification challenge.
    • Graph-search methods provide efficient solutions for protein structure analysis.

    Conclusions:

    • The developed algorithms enhance the capabilities of the ARP/wARP software for automatic model building.
    • This work contributes to more efficient protein structure determination through computational methods.
    • The presented approach offers a robust solution for analyzing chain conformations in structural biology.