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

11.8K
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...
11.8K
Conservation of Protein Domains02:26

Conservation of Protein Domains

2.9K
2.9K
Protein Networks02:26

Protein Networks

3.7K
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,...
3.7K
Protein Networks02:26

Protein Networks

1.8K
1.8K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.1K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

1.0K
1.0K

You might also read

Related Articles

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

Sort by
Same author

High mobility group box 1 (HMGB1) levels in the placenta and in serum in preeclampsia.

American journal of reproductive immunology (New York, N.Y. : 1989)·2011
Same author

Destabilization of coxsackievirus b3 genome integrated with enhanced green fluorescent protein gene.

Intervirology·2011
Same author

[Clinicopathological features of primary splenic histiocytic sarcoma: a case report and literature review].

Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi·2011
Same author

[Comparison of treatment with micro endoscopic discectomy and posterior lumbar interbody fusion using single and double B-Twin expandable spinal spacer].

Zhonghua wai ke za zhi [Chinese journal of surgery]·2011
Same author

Virtual transplantation in designing a facial prosthesis for extensive maxillofacial defects that cross the facial midline using computer-assisted technology.

The International journal of prosthodontics·2011
Same author

Total synthesis of phorboxazole A via de novo oxazole formation: convergent total synthesis.

Journal of the American Chemical Society·2010

Related Experiment Video

Updated: May 3, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K

Principal components analysis of protein sequence clusters.

Bo Wang1, Michael A Kennedy

  • 1Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.

Journal of Structural and Functional Genomics
|February 6, 2014
PubMed
Summary
This summary is machine-generated.

Identifying key amino acid positions driving protein family sub-clustering is challenging. This study introduces a novel sequence conversion algorithm for Principal Component Analysis (PCA), simplifying the identification of critical variations in large protein datasets.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

2.7K
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

3.1K

Related Experiment Videos

Last Updated: May 3, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

2.7K
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

3.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Sequence analysis of large protein families often reveals sub-clusters.
  • Identifying specific amino acid positions responsible for these sub-clusters is crucial but challenging.
  • Principal Component Analysis (PCA) is a powerful dimensionality reduction technique for complex data like protein sequences.

Purpose of the Study:

  • To develop and validate a new algorithm for converting amino acid sequences into a numerical format suitable for PCA.
  • To demonstrate the algorithm's effectiveness in identifying key amino acid positions driving sub-clustering in protein families.
  • To address the limitations of traditional single-letter codes for PCA input.

Main Methods:

  • Development of a novel amino acid sequence conversion algorithm.
  • Application of Principal Component Analysis (PCA) to numerical sequence representations.
  • Validation using an artificial dataset, a small protein family (COG2263), and a large protein family (Pfam04237).

Main Results:

  • The new algorithm successfully converts protein sequence data for PCA.
  • PCA effectively identifies sub-clusters within protein families based on the converted sequences.
  • The method demonstrated its capability in analyzing both small and large protein sequence families, including Pfam04237 with over 1,800 sequences.

Conclusions:

  • The developed algorithm facilitates the application of PCA to protein sequence analysis.
  • This approach enables precise identification of amino acid positions critical for protein family diversification.
  • The method offers a valuable tool for understanding evolutionary relationships and functional divergence in large protein families.