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

Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
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

Proteomics-Based Investigation of Different Live Prey Administered to Freshwater Dark Sleeper (<i>Odontobutis potamophila</i>): Examining the Effects on Glycolipids and Energy Metabolism.

Metabolites·2024
Same author

Transcriptome analysis of immune response against Siniperca chuatsi rhabdovirus infection in mandarin fish Siniperca chuatsi.

Journal of fish diseases·2021
Same author

A Gram-Negative Bacterial Secreted Protein Types Prediction Method Based on PSI-BLAST Profile.

BioMed research international·2016
Same author

Endoplasmic Reticulum Stress May Play a Pivotal Role in Lipid Metabolic Disorders in a Novel Mouse Model of Subclinical Hypothyroidism.

Scientific reports·2016
Same author

Similarity/Dissimilarity analysis of protein sequences based on a new spectrum-like graphical representation.

Evolutionary bioinformatics online·2014
Same author

A protein structural classes prediction method based on PSI-BLAST profile.

Journal of theoretical biology·2014

Related Experiment Video

Updated: May 7, 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

A protein structural classes prediction method based on predicted secondary structure and PSI-BLAST profile.

Shuyan Ding1, Yan Li2, Zhuoxing Shi2

  • 1Department of Sciences, Dalian Nationalities University, Dalian, Liaoning 116600, PR China.

Biochimie
|September 27, 2013
PubMed
Summary

This study introduces a new method using evolutionary and structural features to predict protein secondary structural classes, particularly for low-similarity sequences. The developed approach demonstrates effectiveness in classifying protein structures.

Keywords:
Feature selectionPosition-specific scoring matrixSupport vector machine

More Related Videos

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

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: May 7, 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

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

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:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Understanding protein secondary structural classes is crucial for deciphering protein folding patterns.
  • Accurate prediction of protein structure is a fundamental challenge in molecular biology.

Purpose of the Study:

  • To develop an effective method for predicting protein secondary structural classes, especially for sequences with low similarity.
  • To integrate evolutionary information and predicted structural features for improved prediction accuracy.

Main Methods:

  • A 36-dimensional feature vector was constructed using 25 position-specific scoring matrix (PSSM) features and 11 predicted secondary structure features.
  • The method, termed PSSS-PSSM, was trained on the ASTRALtraining dataset.
  • Performance was evaluated on ASTRALtest, 25PDB, and 1189 low-similarity datasets.

Main Results:

  • The proposed method achieved effective prediction of protein secondary structural classes.
  • Comparisons with existing methods indicated the superiority of the PSSS-PSSM approach for low-similarity sequences.
  • The standalone PSSS-PSSM software is available for download.

Conclusions:

  • The integration of PSSM-based evolutionary information and predicted secondary structure features enhances the accuracy of protein secondary structural class prediction.
  • The PSSS-PSSM method provides a valuable tool for structural bioinformatics research.
  • The developed method is effective for classifying protein structures with limited sequence homology.