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 Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.7K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.7K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

4.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
4.7K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.6K
3.6K
Two-dimensional Gel Electrophoresis01:22

Two-dimensional Gel Electrophoresis

6.9K
Two-dimensional gel electrophoresis is a high-resolution protein separation method first introduced by O' Farrell and Klose in 1975. This method involves protein separation by two dimensions, mass and charge, making it more accurate than one-dimensional gel electrophoresis.
The first dimension separation uses the isoelectric focusing or IEF technique performed on immobilized pH gradient (IPG) strips that separate proteins according to their isoelectric points.
Biological samples, such...
6.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.2K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.2K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.2K
4.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Obstructive Sleep Apnea Screening in Patients Attending Medical Outpatient Department of Tertiary Care Hospital of Kathmandu: A Cross-sectional Study.

JNMA; journal of the Nepal Medical Association·2026
Same author

Global metagenomics reveals plastid diversity and unexplored algal lineages.

Nature communications·2026
Same author

Caffeine in Preterm Infants and its Effect on Neonatal Sleep: A Systematic Review.

Journal of clinical pharmacology·2025
Same author

Well-resolved phylogeny supports repeated evolution of keel flowers as a synergistic contributor to papilionoid legume diversification.

The New phytologist·2025
Same author

Plastid-nuclear coevolution of ribosomal protein genes in papilionoid legumes.

Molecular phylogenetics and evolution·2024
Same author

Successful task shifting: a mixed-methods cross-sectional evaluation of an emergency obstetric care program to increase access to cesarean sections in rural Nepal.

Global health action·2024
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026
Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Nov 22, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

649

DISTEVAL: a web server for evaluating predicted protein distances.

Badri Adhikari1, Bikash Shrestha2, Matthew Bernardini2

  • 1Department of Computer Science, University of Missouri-St. Louis, 312 Express Scripts Hall, St. Louis, MO, USA. adhikarib@umsl.edu.

BMC Bioinformatics
|January 7, 2021
PubMed
Summary
This summary is machine-generated.

A new web server, DISTEVAL, visually evaluates protein inter-residue distance predictions. This tool offers insights beyond numerical metrics, aiding in assessing protein structure prediction accuracy.

Keywords:
Distance predictionDistogramInter-residue contact assessmentInter-residue contact predictionProtein structure prediction

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

15.8K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.4K

Related Experiment Videos

Last Updated: Nov 22, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

649
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

15.8K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.4K

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Prediction

Background:

  • Protein inter-residue contact and distance prediction are crucial for accurate protein structure prediction.
  • Existing evaluation methods for distance predictions lack detailed structural insights.
  • New tools are needed to complement numerical metrics for assessing prediction quality.

Purpose of the Study:

  • To develop a novel web server for evaluating predicted inter-residue distances.
  • To provide visual and qualitative assessment methods for protein distance predictions.
  • To offer a tool that complements existing numerical evaluation metrics.

Main Methods:

  • Development of the DISTEVAL web server.
  • Inputting predicted contacts, distances, and optionally, true structures.
  • Generating visualizations including heatmaps, chord diagrams, and 3D models.

Main Results:

  • DISTEVAL provides informative heatmaps, chord diagrams, and 3D models for visual assessment.
  • The server evaluates predictions using standard metrics like mean absolute error and contact precision.
  • Outputs facilitate both visual and qualitative evaluation of predicted inter-residue distances.

Conclusions:

  • DISTEVAL visualizations offer complementary insights for assessing predicted contacts and distances.
  • The tool enables powerful quantitative and qualitative assessments.
  • DISTEVAL is valuable even when a true 3D structure is unavailable.