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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...

Conservation of Protein Domains

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Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Improving Translational Accuracy

Improving Translational Accuracy

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Related Experiment Video

Updated: Nov 7, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models.

Milton Silva^1,2, Diogo Pratas^1,2,3, Armando J Pinho^1,2

¹IEETA-Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal.

Entropy (Basel, Switzerland)

|April 30, 2021

Summary

This summary is machine-generated.

A new protein sequence compressor, AC2, offers improved compression ratios and reduced memory usage compared to previous methods. This tool also aids in analyzing viral protein similarities, like those in SARS-CoV-2.

Keywords:

context mixing coronavirus lossless data compression mixture of experts neural networks protein sequence compression

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

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Published on: January 26, 2024

Area of Science:

Bioinformatics
Computational Biology
Data Compression

Background:

The rapid growth of protein sequence data presents challenges for storage and analysis.
Existing protein sequence compressors offer limited improvements over general-purpose tools.

Purpose of the Study:

Introduce AC2, a novel lossless data compressor for protein sequences.
Enhance data compression efficiency and enable new analytical applications for biological sequences.

Main Methods:

AC2 employs a neural network with a stacked generalization approach.
It integrates expert models and cache-hash memory for high-context orders.
The compressor was benchmarked against the previous AC compressor.

Main Results:

AC2 achieves 2-9% and 6-7% compression gains in reference-free and reference-based modes, respectively.
It demonstrates a seven-fold reduction in memory usage compared to AC.
AC2 computation is three times slower than AC.

Conclusions:

AC2 provides significant improvements in compression ratio and memory efficiency for protein sequences.
The tool's application in analyzing SARS-CoV-2 similarities offers insights into viral evolution.
AC2 represents a valuable advancement for bioinformatics data management and analysis.