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

Predicting Molecular Geometry02:27

Predicting Molecular Geometry

36.0K
VSEPR Theory for Determination of Electron Pair Geometries
36.0K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.1K
Conserved Binding Sites01:49

Conserved Binding Sites

1.1K
1.1K
Structural Classification of Joints01:20

Structural Classification of Joints

8.1K
Joints, also known as articulations, are classified based on their structural characteristics, i.e., based on whether the articulating surfaces of the adjacent bones are directly connected by fibrous connective tissue or cartilage, or whether the articulating surfaces contact each other within a fluid-filled joint cavity. These differences serve to divide the joints of the body into three structural classifications.
A fibrous joint is where the adjacent bones are united by fibrous connective...
8.1K
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation01:24

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

1.5K
This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
1.5K
Determination of Crystal Structures01:29

Determination of Crystal Structures

139
In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
139

You might also read

Related Articles

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

Sort by
Same author

zelll: a fast, framework-free, and flexible implementation of the cell lists algorithm for the Rust programming language.

Bioinformatics advances·2026
Same author

Sarcomere analysis in human cardiomyocytes by computing radial frequency spectra.

Biological chemistry·2025
Same author

Using Bayesian priors to overcome non-identifiablility issues in Hidden Markov models.

bioRxiv : the preprint server for biology·2025
Same author

Probing the Dynamics of Yersinia Adhesin A (YadA) in Outer Membranes Hints at Requirements for β-Barrel Membrane Insertion.

Journal of the American Chemical Society·2025
Same author

Bayesian multi-exposure image fusion for robust high dynamic range ptychography.

Optics express·2024
Same author

3D Computational Modeling of Defective Early Endosome Distribution in Human iPSC-Based Cardiomyopathy Models.

Cells·2024

Related Experiment Video

Updated: May 6, 2026

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

70.1K

Confidence-guided local structure prediction with HHfrag.

Ivan Kalev1, Michael Habeck

  • 1Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Plos One
|October 23, 2013
PubMed
Summary

This study introduces a new method to reliably predict local protein structure from sequence. It uses a greedy algorithm to filter fragments, improving accuracy for conserved motifs and predicting torsion angles better than current machine learning approaches.

More Related Videos

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD
13:34

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Published on: December 30, 2016

11.1K
Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

1.6K

Related Experiment Videos

Last Updated: May 6, 2026

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

70.1K
Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD
13:34

Production, Crystallization and Structure Determination of C. difficile PPEP-1 via Microseeding and Zinc-SAD

Published on: December 30, 2016

11.1K
Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

1.6K

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Accurate local structure prediction is crucial for understanding protein function.
  • Existing methods struggle with reliability and accuracy, especially for conserved regions.
  • Fragment libraries are a key component in many structure prediction pipelines.

Purpose of the Study:

  • To develop a robust method for assessing local structure prediction reliability from sequence.
  • To improve the accuracy of predicting protein torsion angles using sequence information.
  • To identify conserved motifs within protein sequences based on fragment analysis.

Main Methods:

  • A greedy algorithm for filtering and enriching dynamic fragment libraries.
  • Integration with remote-homology detection methods (e.g., HHfrag).
  • Analysis of fragment recurrence and structural homogeneity to predict conserved motifs.

Main Results:

  • A minimal set of representative fragments with guaranteed correct local structure in conserved regions.
  • Successful prediction of conserved motif locations by analyzing fragment properties.
  • A novel confidence score correlating with local RMSD, outperforming existing machine learning methods in torsion angle prediction.

Conclusions:

  • The developed method enhances the reliability of local structure prediction from sequence.
  • It provides a more accurate approach for predicting torsion angles compared to current techniques.
  • This approach offers a powerful tool for identifying conserved regions and motifs in proteins.