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

Structure-based function inference using protein family-specific fingerprints.

Deepak Bandyopadhyay1, Jun Huan, Jinze Liu

  • 1Department of Computer Science, University of North Carolina at Chapel Hill, North Carolina 27599, USA.

Protein Science : a Publication of the Protein Society
|May 30, 2006
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

Structural characterization and functional evaluation of deer sinew peptide-calcium chelate for intestinal calcium transport and osteogenic differentiation.

International journal of biological macromolecules·2026
Same author

Machine Learning Models with a Reject Option to Minimize Prediction Error: Application to Optical Properties of Dye Molecules.

Research square·2026
Same author

The ROBOKOP v1.0 knowledge graph system for exploring relationships between biomedical entities.

Scientific reports·2026
Same author

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

Cell press blue·2026
Same author

CD38⁺ endothelial remodeling marks spatially patterned vasculopathy in rapidly advancing periodontitis and peri-implantitis.

Nature communications·2026
Same author

E-PTES-S: Enhanced Trust Evaluation via Multidimensional Spatiotemporal Fusion and Variance-Based Stability Sequence Extraction in IoT Sensing Networks.

Sensors (Basel, Switzerland)·2026
Same journal

Macromolecular crowding inhibits degradation of alpha-synuclein amyloid fibrils induced by cathepsins and MMP9.

Protein science : a publication of the Protein Society·2026
Same journal

Sequence-encoded differences in the conformational ensembles of CITED transcriptional activation domains impact coactivator binding.

Protein science : a publication of the Protein Society·2026
Same journal

The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization.

Protein science : a publication of the Protein Society·2026
Same journal

Structural basis of ligand selectivity in FAD/NAD(P)H-dependent dehydrogenases: insights from trypanothione reductase and type II NADH dehydrogenase.

Protein science : a publication of the Protein Society·2026
Same journal

Achieving protease substrate-specific inhibition by mAb dual functional selections.

Protein science : a publication of the Protein Society·2026
Same journal

How important are quantum mechanical effects in controlling biological functions: Enzymes, electron transfer and bird navigation.

Protein science : a publication of the Protein Society·2026
See all related articles

This study introduces a novel protein structure classification method using unique amino acid packing patterns called fingerprints. This approach accurately assigns protein structures to functional families, aiding in function prediction for uncharacterized proteins.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein functional annotation

Background:

  • Assigning protein structures to functional families is crucial for understanding biological roles.
  • Existing methods rely on sequence or structural similarity, which can be insufficient for divergent families.
  • There is a need for complementary methods to improve protein function prediction accuracy.

Purpose of the Study:

  • To develop and validate a novel method for assigning protein structures to functional families using family-specific fingerprints.
  • To enhance the accuracy of protein function prediction, particularly for novel and orphan proteins.
  • To demonstrate the utility of fingerprints as a complementary approach to existing classification techniques.

Main Methods:

Related Experiment Videos

  • Frequent Subgraph Mining was employed to derive family-specific fingerprints from 120 SCOP families.
  • A fast subgraph isomorphism algorithm was used to identify fingerprint occurrences in new protein structures.
  • Confidence values were calculated based on fingerprint count and background distribution for family assignment.

    • Main Results:

    • The method successfully assigned protein structures to functional families with high confidence.
    • Validation experiments demonstrated accurate inference of function for new SCOP family members.
    • The approach effectively discriminated between structurally similar but functionally distinct TIM barrel families.

    Conclusions:

    • Family-specific fingerprints offer a powerful and complementary approach for protein structure-function relationship studies.
    • This method improves the accuracy of protein function prediction, including for structural genomics and orphan proteins.
    • The findings have significant implications for biological discovery and protein annotation databases.