Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

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

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026

Same author

How Not to be Seen: Predicting Unseen Enzyme Functions using Contrastive Learning.

bioRxiv : the preprint server for biology·2026

Same author

A PLUM Job: Peptide modeLs for Understanding and engineering antiMicrobial therapeutics.

bioRxiv : the preprint server for biology·2026

Same author

Advances in Protein Function Prediction from the Fifth CAFA Challenge.

bioRxiv : the preprint server for biology·2026

Same author

LAFA: A Framework for Reproducible Longitudinal Assessment of Protein Function Annotation Models.

ArXiv·2026

Same author

EpicTope: predicting and validating non-disruptive epitope tagging sites.

Development (Cambridge, England)·2026

Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026

Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026

Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026

Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026

Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026

Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 13, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Fragnostic: walking through protein structure space.

Iddo Friedberg¹, Adam Godzik

¹The Burnham Institute 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. idoerg@burnham.org

Nucleic Acids Research

|June 28, 2005

Summary

This summary is machine-generated.

Fragnostic is a web tool that reveals hidden connections between proteins by analyzing shared structural fragments. It maps protein fold similarity, aiding in the discovery of distant evolutionary and functional relationships.

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Jan 13, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Structural bioinformatics
Computational biology
Protein structure analysis

Background:

Understanding protein structure-function relationships is crucial in biology.
Identifying similarities between proteins with different folds can reveal evolutionary links.
Existing methods may not fully capture distant relationships based on shared substructures.

Purpose of the Study:

To introduce the Fragnostic web tool for exploring protein structure space.
To develop a novel method for measuring inter-fold similarity based on shared protein fragments.
To facilitate the discovery of structural and functional relationships between distantly related proteins.

Main Methods:

Mining the Protein Data Bank (PDB) for common fragments across different SCOP folds.
Formulating an inter-fold similarity measure based on the extent of fragment sharing.
Representing protein fold space as a graph where nodes are folds and edges represent fragment sharing.

Main Results:

The Fragnostic tool provides a novel visualization of protein structure space.
Identified meaningful relationships between proteins belonging to different folds through fragment sharing.
Successfully supplemented distant fold similarity data with annotations from Gene Ontology, SCOP, and CATH.

Conclusions:

Fragnostic offers a unique approach to uncovering relationships between seemingly unrelated proteins.
The tool aids in discovering structural and functional similarities based on shared protein fragments.
Fragnostic enhances our understanding of protein evolution and function by connecting diverse protein families.