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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a 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...

You might also read

Related Articles

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

Sort by
Same author

Preoperative Intravitreal Conbercept Facilitates Vitrectomy in Proliferative Diabetic Retinopathy: Is Attention Required for the Fellow Eye?

Journal of ophthalmology·2019
Same author

Low-dose statin pretreatment reduces stroke severity and improves functional outcomes.

Journal of neurology·2019
Same author

Nanotribological Properties of Ga- and N-Faced Bulk Gallium Nitride Surfaces Determined by Nanoscratch Experiments.

Materials (Basel, Switzerland)·2019
Same author

Genetic Diversity and Population Structure Analysis of Three Deep-Sea Amphipod Species from Geographically Isolated Hadal Trenches in the Pacific Ocean.

Biochemical genetics·2019
Same author

Properties and Reaction Mechanisms of Magnesium Phosphate Cement Mixed with Ferroaluminate Cement.

Materials (Basel, Switzerland)·2019
Same author

Zein Particle-Stabilized Water-In-Water Emulsion as a Vehicle for Hydrophilic Bioactive Compound Loading of Riboflavin.

Journal of agricultural and food chemistry·2019

Related Experiment Video

Updated: Jul 3, 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

PairProSVM: protein subcellular localization based on local pairwise profile alignment and SVM.

Man-Wai Mak1, Jian Guo, Sun-Yuan Kung

  • 1Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong. enmwmak@polyu.edu.hk

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|August 2, 2008
PubMed
Summary
This summary is machine-generated.

A new computational method, PairProSVM, accurately predicts protein subcellular locations. This tool enhances proteomics research by offering a reliable approach to understanding protein function based on their cellular destinations.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Jul 3, 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

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Subcellular localization is crucial for understanding protein function.
  • Accurate prediction methods are essential for large-scale proteomics studies.
  • Existing methods have limitations in accuracy and reliability.

Purpose of the Study:

  • To introduce PairProSVM, a novel computational method for automated subcellular localization prediction.
  • To evaluate the performance of PairProSVM against existing techniques.
  • To analyze the factors influencing PairProSVM's predictive accuracy.

Main Methods:

  • Utilizing PSI-BLAST to generate protein sequence profiles.
  • Employing pairwise profile-alignment scores to create feature vectors.
  • Training a support vector machine (SVM) classifier with these feature vectors.

Main Results:

  • PairProSVM demonstrated superior performance compared to sequence alignment and amino-acid composition methods.
  • Performance remained high even after removing homologous sequences.
  • Achieved high accuracies: 99.3% (Reinhardt and Hubbard), 76.5% (Huang and Li), and 91.9% (Gardy et al.).

Conclusions:

  • PairProSVM offers a highly effective and reliable method for predicting protein subcellular localization.
  • The method's performance is influenced by the kernel matrix properties.
  • PairProSVM provides a valuable tool for advancing proteomics research and protein function annotation.