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

Unsymmetric Bending - Angle of Neutral Axis01:15

Unsymmetric Bending - Angle of Neutral Axis

Unsymmetrical bending occurs when a structural member is subjected to bending moments in a plane that does not align with the member's principal axes. This scenario typically arises in beams and other structural components when loads are applied at non-ideal angles, introducing complexities in stress analysis.
When a bending moment is applied at an angle θ concerning the vertical axis of a symmetrical member, it can be resolved into components along the member's principal centroidal axes. The...
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
Angle of Twist: Problem Solving01:13

Angle of Twist: Problem Solving

An electric motor applies a torque of 700 N·m to an aluminum shaft, triggering a stable rotation. Two pulleys, B and C, are subjected to torques of 300 N·m and 400 N·m, respectively. The modulus of rigidity is provided as 25 GPa. With the knowledge of the length and diameter of each segment, the twist angle between the two pulleys can be computed. First, a section cut is made between pulleys B and C, and the cut cross-section is analyzed using a free-body diagram. Given that the torque exerted...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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 form...
Angle of Twist - Elastic Range01:13

Angle of Twist - Elastic Range

Consider a cylindrical shaft with a length denoted by L and a consistent cross-sectional radius referred to as r. This shaft undergoes a torque at the free end. The highest shearing strain within the shaft is directly proportional to the twist angle and the radial distance from the shaft axis. When the shaft behaves elastically, this shearing strain can be articulated using variables such as the applied torque, radial distance, the polar moment of inertia, and the modulus of rigidity. By...
Protein Folding01:22

Protein Folding

Overview

You might also read

Related Articles

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

Sort by
Same author

Case report: Deep sequencing and long-read genome sequencing refine prior genetic analyses in families with apparent gonadal mosaicism in <i>PIK3CD</i>-related activated PI3K delta syndrome.

Frontiers in immunology·2024
Same author

Reticular dysgenesis caused by an intronic pathogenic variant in <i>AK2</i>.

Cold Spring Harbor molecular case studies·2020
Same author

<i>NUBPL</i> mitochondrial disease: new patients and review of the genetic and clinical spectrum.

Journal of medical genetics·2020
Same author

Gene family information facilitates variant interpretation and identification of disease-associated genes in neurodevelopmental disorders.

Genome medicine·2020
Same author

Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes.

NPJ precision oncology·2020
Same author

Targeting cellular heterogeneity with CXCR2 blockade for the treatment of therapy-resistant prostate cancer.

Science translational medicine·2019

Related Experiment Video

Updated: Jun 28, 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

ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction.

Sitao Wu1, Yang Zhang

  • 1Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS, USA.

Plos One
|October 17, 2008
PubMed
Summary
This summary is machine-generated.

We developed ANGLOR, a machine learning algorithm that predicts protein backbone torsion angles from amino acid sequences. This tool shows improved accuracy, aiding in protein structure modeling.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: Jun 28, 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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Machine Learning in Structural Biology

Background:

  • Accurate prediction of protein backbone torsion angles is crucial for determining 3D protein structures.
  • Existing methods for predicting torsion angles from amino acid sequences have limitations in accuracy.

Purpose of the Study:

  • To develop a novel machine learning algorithm, ANGLOR, for predicting real-value protein backbone torsion angles (phi/psi) from amino acid sequences.
  • To evaluate the performance of ANGLOR against existing computational tools and random prediction methods.

Main Methods:

  • ANGLOR utilizes a composite machine learning approach.
  • Input features include sequence profiles, predicted secondary structure, and solvent accessibility.
  • Performance was assessed using Mean Absolute Error (MAE) and Wilcoxon signed rank test.

Main Results:

  • ANGLOR achieved a Mean Absolute Error (MAE) of 28 degrees for phi angles and 46 degrees for psi angles.
  • This represents an approximate 10% improvement in accuracy compared to existing software.
  • Predictions were statistically significant (p-value <1.0 x 10(-300) for phi, p-value <1.0 x 10(-148) for psi) compared to random predictors.
  • Higher accuracy was observed for specific residues (ILE, LEU, PRO, VAL) and in helix/buried regions (10-20 degrees MAE for phi).

Conclusions:

  • ANGLOR demonstrates improved accuracy in predicting protein backbone torsion angles.
  • While average accuracy is still limited, the accurately predicted angles can assist in protein fold recognition and ab initio 3D structure modeling.
  • The algorithm's performance highlights the potential of machine learning in advancing structural bioinformatics.