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

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.

M G Williams1, H Shirai, J Shi

  • 1Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Proteins
|February 9, 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

Receptor based virtual screening of potential novel inhibitors of tigar [TP53 (tumour protein 53)-induced glycolysis and apoptosis regulator.

Medical hypotheses·2021
Same author

Reply to the comments by Falsetti et al.

Reumatismo·2020
Same author

Subcalcaneal bursitis as the initial manifestation of rheumatoid arthritis: ultrasonographic observation of two cases.

Reumatismo·2020
Same author

The Molecular Basis for Antigenic Drift of Human A/H2N2 Influenza Viruses.

Journal of virology·2019
Same author

Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as glucono-lactonase in pentose phosphate pathway and glucose metabolism.

Bioinformation·2018
Same author

CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.

Bioinformatics (Oxford, England)·2017
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

This study presents FUGUE, a protein structure prediction method using sequence-structure homology recognition and environment-specific substitution tables. The approach achieved high scores in the CASP4 experiment by rigorously evaluating predicted protein models.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure prediction is crucial for understanding protein function.
  • Accurate prediction of protein three-dimensional structures remains a significant challenge in bioinformatics.
  • The Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments benchmark prediction methods.

Purpose of the Study:

  • To evaluate the FUGUE program for sequence-structure homology recognition in protein structure prediction.
  • To assess the effectiveness of environment-specific substitution tables in protein modeling.
  • To improve the accuracy of protein model building and evaluation.

Main Methods:

  • Utilized the FUGUE sequence-structure homology recognition program.

Related Experiment Videos

  • Developed and applied environment-specific substitution tables derived from the HOMSTRAD database.
  • Incorporated structural information into sequence profiles using HOMSTRAD alignments.
  • Employed JOY for annotating sequence alignments with local structural features.
  • Rigorous evaluation and rejection of incorrect protein models.

    • Main Results:

    • FUGUE successfully performed sequence-structure homology recognition.
    • Environment-specific substitution tables enhanced the modeling and evaluation procedures.
    • JOY annotation aided in hypothesis refinement and prediction rejection.
    • The stringent model rejection strategy minimized false positives, leading to a high average score in CASP4.

    Conclusions:

    • The FUGUE approach, incorporating environment-specific substitution tables and JOY annotation, is effective for protein structure prediction.
    • Rigorous model evaluation is critical for achieving high accuracy in protein structure prediction.
    • This method demonstrated strong performance in the CASP4 experiment.