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

Protein structure comparison by alignment of distance matrices

L Holm1, C Sander

  • 1European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany.

Journal of Molecular Biology
|September 5, 1993
PubMed
Summary

The DALI algorithm accurately compares protein structures by analyzing distance matrices. This novel method reveals hidden structural similarities, aiding in the classification of protein folds.

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

Depressive and anxiety symptoms in individuals with Long-COVID: Does social network matter? - Results of a German Long-COVID study.

Journal of affective disorders·2026
Same author

Do values and political attitudes affect help-seeking? Exploring reported help-seeking for mental health problems in a general population sample using a milieu framework.

Epidemiology and psychiatric sciences·2023
Same author

Serum BDNF levels correlate with regional cortical thickness in minor depression: a pilot study.

Scientific reports·2020
Same author

Measurements of the associated production of a Z boson and b jets in pp collisions at <math> </math>.

The European physical journal. C, Particles and fields·2020
Same author

Study of Jet Quenching with Z+jet Correlations in Pb-Pb and pp Collisions at sqrt[s]_{NN}=5.02  TeV.

Physical review letters·2017
Same author

Searches for pair production of third-generation squarks in [Formula: see text][Formula: see text] pp collisions.

The European physical journal. C, Particles and fields·2017

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • The increasing number of known protein tertiary structures necessitates advanced methods for structural comparison.
  • Protein structure comparison is crucial for understanding protein function, evolution, and classification.

Purpose of the Study:

  • To develop a novel algorithm for optimal pairwise alignment of protein structures.
  • To accurately and sensitively identify structural resemblances and common structural cores.

Main Methods:

  • Utilized 3D coordinates to compute residue-residue distance matrices.
  • Decomposed matrices into contact patterns and paired similar patterns.
  • Employed a Monte Carlo procedure to optimize similarity scores based on intramolecular distances.

Related Experiment Videos

Main Results:

  • Developed the DALI algorithm for protein structure alignment.
  • The method handles sequence gaps, chain reversals, and flexible topological connectivity.
  • An all-against-all alignment classified over 200 protein structures, agreeing with visual classifications.
  • Detected novel topological similarities, such as between colicin A and globins.

Conclusions:

  • DALI provides an accurate and sensitive method for protein structure comparison.
  • The algorithm facilitates objective classification of three-dimensional protein folds.
  • Identified biologically significant structural similarities previously unrecognized.