Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Signal Sequences and Sorting Receptors

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...

Protein Families

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...

You might also read

Related Articles

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

Sort by

Same author

Age, sex, and regional disparities in vision impairment burden among the population with diabetes: a 10-year trend analysis in Taiwan.

Eye (London, England)·2026

Same author

Physalin A interferes with cell cycle in human oral squamous carcinoma cells via DNA topoisomerase II/ATM/ATR/Chk signaling for G2/M phase arrest.

Archives of biochemistry and biophysics·2026

Same author

Trajectories of metabolic risk clusters and adverse outcomes in patients with chronic kidney disease: a prospective cohort study in Taiwan.

BMJ open·2026

Same author

scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Bioinformatics (Oxford, England)·2026

Same author

Multicentre, retrospective observational study on risk factors of major cardiovascular adverse events in patients with chronic kidney disease in Taiwan.

BMJ open·2026

Same author

Reactive oxygen species driven immune inflammation in systemic sclerosis: mechanisms and emerging therapeutics.

Drug discovery today·2026

Same journal

Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2.

Computational and structural biotechnology journal·2026

Same journal

From Pixels to Patterns: A Multidimensional Framework to Decode Cytoskeletal Organization.

Computational and structural biotechnology journal·2026

Same journal

A Large Concept Model for Mechanistic Simulation of Disease Trajectories: A Hypothesis-Generating Exemplar for Pediatric Acute Lymphoblastic Leukemia.

Computational and structural biotechnology journal·2026

Same journal

Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design.

Computational and structural biotechnology journal·2026

Same journal

High-Throughput Prediction of Protein-Protein Interactions Uncovers Hidden Molecular Networks in Biosynthetic Gene Clusters.

Computational and structural biotechnology journal·2026

Same journal

A Region-Aware Structured Framework Improves Prediction of Gene Expression from DNA Methylation.

Computational and structural biotechnology journal·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Aug 15, 2025

Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

SeqCP: A sequence-based algorithm for searching circularly permuted proteins.

Chi-Chun Chen^1,2, Yu-Wei Huang³, Hsuan-Cheng Huang^1,4

¹Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan.

Computational and Structural Biotechnology Journal

|December 30, 2022

Summary

This summary is machine-generated.

SeqCP identifies circular permutation (CP) in proteins using sequence alignments, advancing protein studies and bioengineering. This method helps find circularly permuted protein pairs (CPMs) even without structural data.

Keywords:

AUC, area under the ROC curve CE, combinatorial extension CE-CP, CE with Circular Permutations CP, circular permutation CPDB, Circular Permutation Database CPMs, circular permutants CPSARST, Circular Permutation Search Aided by Ramachandran Sequential Transformation Circular permutants Circular permutation MCC, Matthews correlation coefficient Protein sequence analysis Protein structure modeling RMSD, root-mean-square distance ROC, receiver operating characteristic

More Related Videos

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Related Experiment Videos

Last Updated: Aug 15, 2025

Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Area of Science:

Proteomics
Bioinformatics
Structural Biology

Background:

Circular permutation (CP) rearranges protein termini, often preserving structure and function.
Current CP detection relies heavily on protein structures, limiting identification for proteins lacking structural data.

Purpose of the Study:

To develop an efficient sequence-based method for identifying circularly permuted protein pairs (CPMs).
To overcome limitations of structure-based methods for CP detection, especially for proteins with unknown structures.

Main Methods:

Developed SeqCP, a sequence-based algorithm analyzing normal and duplicated sequence alignments.
Trained SeqCP using data from the Circular Permutation Database.
Tested SeqCP on nonredundant datasets from the Protein Data Bank.

Main Results:

SeqCP demonstrates high reliability in identifying CPMs.
Achieved an Area Under the Curve (AUC) of 0.9, indicating strong performance.
Identified candidate CP sites within protein sequences.

Conclusions:

SeqCP offers a valuable tool for discovering CPMs using only sequence information.
This method facilitates functional annotation and bioengineering applications for proteins lacking structural data.
A web server for SeqCP is available at http://pcnas.life.nthu.edu.tw/SeqCP/.