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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...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Related Experiment Video

Updated: Jun 19, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
16:02

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

Published on: February 10, 2023

Several appropriate background distributions for entropy-based protein sequence conservation measures.

Yongchao Dou1, Xiaoqi Zheng, Jun Wang

  • 1School of Mathematical Science, Dalian University of Technology, Dalian 116024, PR China.

Journal of Theoretical Biology
|October 8, 2009
PubMed
Summary

Accurate amino acid background distributions improve predictions of functionally important protein residues from multiple sequence alignments (MSAs). New methods enhance sequence conservation analysis for identifying catalytic and ligand binding sites.

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Last Updated: Jun 19, 2026

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

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Amino acid background distribution is crucial for entropy-based methods analyzing protein sequence conservation in multiple sequence alignments (MSAs).
  • Reliable observed background distributions are often unattainable due to insufficient MSA sizes.

Purpose of the Study:

  • To develop and validate novel methods for estimating amino acid background distribution in protein MSAs.
  • To improve the prediction of functionally important residues, such as catalytic and ligand binding sites.

Main Methods:

  • Proposed two new background distribution estimations: 1) integration of observed and position-specific residue distributions, and 2) normalized square root of observed background frequency.
  • Applied these methods to a relative entropy model for identifying functional sites in protein MSAs.

Main Results:

  • The proposed background distribution estimations demonstrated superior performance compared to the observed background distribution.
  • These new methods significantly improved the prediction accuracy of functionally important residues.

Conclusions:

  • The novel background distribution estimations are effective for enhancing sequence conservation analysis in bioinformatics.
  • These approaches offer a more reliable way to identify critical functional sites in proteins using limited MSA data.