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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...
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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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...
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...

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Related Experiment Video

Updated: May 25, 2026

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

An improved scoring method for protein residue conservation and multiple sequence alignment.

Ken D Nguyen1, Yi Pan

  • 1Department of Information Technology, Clayton State University, Morrow, GA 30260, USA. knguyen@clayton.edu

IEEE Transactions on Nanobioscience
|January 25, 2012
PubMed
Summary
This summary is machine-generated.

A new scoring method, hierarchical expected matching probability (HEP), improves biological sequence alignment accuracy. This method simplifies gap cost selection and enhances protein multiple sequence alignment reliability.

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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Last Updated: May 25, 2026

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

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
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Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

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:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial for understanding biological sequence relationships, structure, and function.
  • Accurate MSA relies heavily on effective scoring functions, which can significantly boost alignment precision.
  • Optimizing MSA is computationally challenging, necessitating reliable and efficient scoring methods.

Purpose of the Study:

  • To introduce a novel, fast, and biologically reliable scoring method for protein multiple sequence alignment.
  • To address the limitations of existing scoring functions, particularly the complexity of gap cost selection.
  • To evaluate the performance of the new scoring method against established benchmarks.

Main Methods:

  • Development of the hierarchical expected matching probability (HEP) scoring method.
  • Integration of the HEP method into a progressive multiple sequence alignment algorithm.
  • Testing and validation using four diverse benchmarks: Valdar's theoretical conservation benchmark, RT-OSM, BAliBASE3.0, and PREFAB4.0.

Main Results:

  • The HEP method demonstrated superior biological reliability compared to other tested scoring methods across all benchmarks.
  • Implementation of HEP in a progressive alignment algorithm resulted in accuracy improvements of up to 7% on BAliBASE3.0 and 5% on PREFAB4.0.
  • The HEP scoring method effectively eliminates the need for manual gap cost selection.

Conclusions:

  • The hierarchical expected matching probability (HEP) offers a significant advancement in scoring functions for protein multiple sequence alignment.
  • HEP provides a more accurate and reliable approach to sequence alignment, simplifying the process for researchers.
  • This new method has the potential to enhance the accuracy of various MSA tools and analyses.