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

A novel approach to structural alignment using realistic structural and environmental information.

Yu Chen1, Gordon M Crippen

  • 1College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, MI 48109-1065, USA.

Protein Science : a Publication of the Protein Society
|November 2, 2005
PubMed
Summary

This study introduces SAUCE, a novel structural alignment method incorporating environmental data. SAUCE accurately aligns protein structures, even in different oligomeric states and flexible coil regions.

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

Purely in silico BCS classification: science based quality standards for the world's drugs.

Molecular pharmaceutics·2013
Same author

SAGA: rapid automatic mainchain NMR assignment for large proteins.

Journal of biomolecular NMR·2010
Same author

Predicting pKa.

Journal of chemical information and modeling·2009
Same author

A statistical measure of association and a series expansion of chain conformations.

Computational biology and chemistry·2009
Same author

Ischemic preconditioning attenuates renal ischemia-reperfusion injury by inhibiting activation of IKKbeta and inflammatory response.

American journal of nephrology·2009
Same author

RUVBL2, a novel AS160-binding protein, regulates insulin-stimulated GLUT4 translocation.

Cell research·2009

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Accurate protein structural alignment is crucial for homology modeling in structural genomics.
  • Existing methods often neglect intermolecular interactions, hindering alignment of structures in different oligomeric states and in flexible coil regions.

Purpose of the Study:

  • To develop a novel structural alignment approach that incorporates environmental information.
  • To improve the accuracy of structural alignments, particularly for proteins in different oligomeric states and with flexible regions.

Main Methods:

  • Utilized a clique finding algorithm combined with environmental information (SAUCE).
  • Integrated structural coordinate data with environmental data from Protein Data Bank (PDB) biological unit files.

Related Experiment Videos

  • Developed Extreme Value Distribution (EVD) statistics for core region alignment evaluation and an optional dynamic programming extension for global alignment.

    • Main Results:

    • SAUCE successfully differentiates three-dimensional structures in varying oligomeric states.
    • The method achieves flexible alignments for multidomain structures without requiring predefined hinge regions.
    • Performance evaluation demonstrated competitive results compared to existing methods and databases.

    Conclusions:

    • SAUCE offers a robust approach to protein structural alignment by leveraging environmental context.
    • The method enhances the ability to model homologous proteins and understand structural variations.
    • This approach advances the field of structural bioinformatics and protein structure analysis.