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Conservation of Protein Domains Over Different Proteins

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 Domains

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...

Multi-species Conserved Sequences

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 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 locations, protein...

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 locations, protein...

Conserved Binding Sites

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...

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Related Experiment Video

Updated: Jun 21, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

On subset seeds for protein alignment.

Mikhail Roytberg¹, Anna Gambin, Laurent Noé

¹Institute of Mathematical Problems in Biology, Pushchino, Moscow Region 142290, Russia. mroytberg@mail.ru

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|August 1, 2009

Summary

This summary is machine-generated.

We developed new subset seeds for protein sequence similarity search. These seeds offer comparable or better performance than Blastp, improving efficiency in biological data analysis.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Protein sequence similarity search is crucial for understanding protein function and evolution.
Existing methods like Blastp seeding have limitations in sensitivity and selectivity.
Optimizing seed design is key to improving search algorithm performance.

Purpose of the Study:

To design efficient seed alphabets for subset seeds.
To achieve optimal sensitivity/selectivity trade-offs in protein similarity search.
To compare the performance of novel subset seeds against established methods.

Main Methods:

Developing novel design methods for subset seed alphabets.
Constructing and analyzing seeds based on these alphabets.
Comparative analysis against Blastp seeding and vector seeds.
Large-scale benchmarking on major protein alignment databases.

Main Results:

Subset seeds demonstrate comparable or superior performance to Blastp.
Achieved optimal sensitivity/selectivity trade-offs with efficient seed alphabets.
Performance validated on Bernoulli protein models and real-world databases.
The proposed subset seed formalism is less complex but highly effective.

Conclusions:

Subset seeds represent a promising advancement in protein sequence similarity search.
The developed seed design methods offer practical improvements over current standards.
This approach enhances the efficiency and accuracy of large-scale biological data analysis.