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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...

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Related Experiment Video

Updated: Jun 29, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Rapid multiple protein sequence search by parallel and heterogeneous computation.

Jiefu Li¹, Ziyuan Wang², Xuwei Fan²

¹CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.

Bioinformatics (Oxford, England)

|March 28, 2024

Summary

This summary is machine-generated.

Chorus accelerates protein sequence database searches, offering over 100x speedup compared to BLASTP for large datasets. This novel system enables efficient querying of thousands of protein sequences on a desktop workstation.

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Last Updated: Jun 29, 2025

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Published on: January 26, 2024

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Multi-target Parallel Processing Approach for Gene-to-structure Determination of the Influenza Polymerase PB2 Subunit

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Protein sequence database searching and multiple sequence alignment are crucial in bioinformatics.
Rapidly growing sequence data necessitates efficient and scalable query algorithms for large databases.

Purpose of the Study:

To introduce Chorus, a novel protein sequence query system.
To enable concurrent querying of thousands of protein sequences against large databases on a desktop workstation.
To achieve significant speedup without compromising sensitivity.

Main Methods:

Leveraging a parallel model and heterogeneous computation architecture.
Developing a novel protein sequence query system named Chorus.
Benchmarking against established methods like BLASTP.

Main Results:

Chorus achieves over 100x speedup compared to BLASTP.
Demonstrated utility in analyzing a 1.5-TB metagenomic dataset for novel CRISPR-Cas protein discovery within 30 minutes.
Maintained sensitivity comparable to existing methods.

Conclusions:

Chorus provides a highly efficient and scalable solution for large-scale protein sequence database queries.
The system enables rapid discovery of novel proteins, such as CRISPR-Cas systems, from massive datasets.
Chorus is open-source and accessible for broader research applications.