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

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...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

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...
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 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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
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

Granular support vector machine to identify unknown structural classes of protein.

International journal of data mining and bioinformatics·2015
Same author

Multi-stage filtering for improving confidence level and determining dominant clusters in clustering algorithms of gene expression data.

Computers in biology and medicine·2013
Same author

Iris segmentation using an edge detector based on fuzzy sets theory and cellular learning automata.

Applied optics·2011
Same author

Utilizing shared interacting domain patterns and Gene Ontology information to improve protein-protein interaction prediction.

Computers in biology and medicine·2010
Same author

SPlitSSI-SVM: an algorithm to reduce the misleading and increase the strength of domain signal.

Computers in biology and medicine·2009
Same author

A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences.

Journal of biomedical informatics·2007
Same journal

Corrigendum to "CFPNet-M: A light-weight encoder-decoder based network for multimodal biomedical image real-time segmentation" [Comput. Biol. Med. 154 (2023) 106579].

Computers in biology and medicine·2026
Same journal

ECG arrhythmia classification via wavelet-driven feature extraction and swarm-optimised gradient boosting.

Computers in biology and medicine·2026
Same journal

Electro-osmotic metachronal cilia transport of viscoelastic blood infused with penta-hybrid nanoparticles in an oviduct: Analytical and neural network modeling.

Computers in biology and medicine·2026
Same journal

sEEGnal: an automated EEG preprocessing pipeline evaluated against expert-driven preprocessing.

Computers in biology and medicine·2026
Same journal

Corrigendum to "Integrating experimental biology, computational methods, and artificial Intelligence in anticancer drug discovery: Bridging the translational Gap" [Comput. Biol. Med. 213 (2026) 111832].

Computers in biology and medicine·2026
Same journal

Organ dose optimization for a point-of-care forearm X-ray photon-counting CT.

Computers in biology and medicine·2026
See all related articles

Related Experiment Video

Updated: May 31, 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

Remote protein homology detection and fold recognition using two-layer support vector machine classifiers.

Hilmi M Muda1, Puteh Saad, Razib M Othman

  • 1Laboratory of Computational Intelligence and Biology, Faculty of Computer Science and Information Systems, Universiti Teknologi Malaysia, 81310 UTM Skudai, Malaysia.

Computers in Biology and Medicine
|June 28, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a novel two-layer Support Vector Machine (SVM) method for remote protein homology detection and fold recognition. The approach significantly improves accuracy across multiple datasets, enhancing protein structure classification.

More Related Videos

Image Recognition and Parameter Analysis of Concrete Vibration State Based on Support Vector Machine
08:27

Image Recognition and Parameter Analysis of Concrete Vibration State Based on Support Vector Machine

Published on: January 5, 2024

Related Experiment Videos

Last Updated: May 31, 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

Image Recognition and Parameter Analysis of Concrete Vibration State Based on Support Vector Machine
08:27

Image Recognition and Parameter Analysis of Concrete Vibration State Based on Support Vector Machine

Published on: January 5, 2024

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Bioinformatics

Background:

  • Remote protein homology detection identifies structural similarities with minimal sequence identity.
  • Existing methods include discriminative classifiers, generative models, and pairwise comparisons.
  • Support Vector Machines (SVMs) offer advantages in speed, accuracy, and efficiency over Neural Networks (NNs).

Purpose of the Study:

  • To develop and evaluate a comprehensive, two-layer classification method for remote protein homology detection and fold recognition.
  • To leverage biological information within classification rules for improved accuracy.
  • To assess the method's performance across different versions of the SCOP (Structural Classification of Proteins) database.

Main Methods:

  • A two-layer classifier system (BioSVM-2L) was implemented.
  • The first layer utilizes optimized binary SVMs with a Bio-kernel to classify protein superfamilies and families.
  • The second layer employs SVMs with a string kernel for protein fold level classification.

Main Results:

  • The proposed method demonstrated significant performance improvements in remote homology detection and fold recognition.
  • Mean ROC (Receiver Operating Characteristic) scores showed improvements of 4.19% (SCOP 1.53), 4.75% (SCOP 1.67), and 4.03% (SCOP 1.73).
  • The BioSVM-2L approach proved effective across all tested SCOP dataset versions.

Conclusions:

  • The developed two-layer SVM method enhances remote protein homology detection and fold recognition.
  • Incorporating biological information via the Bio-kernel and string kernel improves classification accuracy.
  • The BioSVM-2L system offers a robust solution for classifying protein structures from primary sequences.