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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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Related Experiment Video

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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

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.

Lisa Bartoli1, Piero Fariselli, Anders Krogh

  • 1Biocomputing Group, Department of Biology, University of Bologna, 40126 Bologna, Italy.

Bioinformatics (Oxford, England)
|September 12, 2009
PubMed
Summary

A new hidden Markov model (CCHMM_PROF) accurately predicts coiled-coil regions in proteins using sequence profiles. This method outperforms existing tools for protein structure and function determination.

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Last Updated: Jun 20, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis
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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

Area of Science:

  • Proteomics
  • Bioinformatics
  • Structural Biology

Background:

  • Coiled-coil motifs are crucial for protein interactions and function.
  • Accurate identification of coiled-coil domains aids in protein structure prediction.
  • Existing prediction tools have limitations in accuracy and efficiency.

Purpose of the Study:

  • To introduce CCHMM_PROF, a novel hidden Markov model for coiled-coil region prediction.
  • To leverage multiple sequence alignments (profiles) for enhanced prediction accuracy.
  • To provide a robust tool for large-scale genome annotation.

Main Methods:

  • Development of a hidden Markov model (CCHMM_PROF).
  • Utilizing protein sequence profiles derived from multiple sequence alignments.
  • Performance evaluation against existing coiled-coil prediction methods.

Main Results:

  • CCHMM_PROF achieves 97% accuracy in discriminating coiled-coil sequences.
  • High true positive rate (79%) with minimal false positives (1%).
  • Residue-level accuracy of 80% and segment/protein efficiency of 81%/80%.

Conclusions:

  • CCHMM_PROF significantly outperforms current coiled-coil prediction tools.
  • The method is suitable for accurate and efficient large-scale genome annotation.
  • The predictor and dataset are publicly available for research use.