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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...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

Protein and Protein Structures

Protein and Protein Structures

Conservation of Protein Domains

Conservation of Protein Domains

Protein Folding

Protein Folding

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Related Experiment Video

Updated: Sep 18, 2025

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

Tokenized and continuous embedding compressions of protein sequence and structure.

Amy X Lu^1,2, Wilson Yan¹, Kevin K Yang³

¹University of California, Berkeley, Berkeley, CA, USA.

Patterns (New York, N.Y.)

|June 27, 2025

Summary

We developed Compressed Hourglass Embedding Adaptations of Proteins (CHEAP) by compressing protein folding model latent spaces. CHEAP embeddings provide interpretable and flexible representations of protein sequence and structure for various applications.

Keywords:

model interpretability neural compression protein language models protein structure tokenization representation learning

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Area of Science:

Computational Biology
Machine Learning
Structural Bioinformatics

Background:

Current protein machine learning models often focus on sequence or structure independently.
Integrating both sequence and structure information is crucial for comprehensive protein representation.

Purpose of the Study:

To develop a compressed, interpretable, and flexible representation of joint protein sequence and structure distributions.
To introduce CHEAP embeddings derived from the ESMFold model's latent space.

Main Methods:

Compressing the latent space of the ESMFold protein folding model using continuous and discrete schemes.
Evaluating the retention of structural information and performance on downstream tasks like function and localization prediction.

Main Results:

Continuous compression reduced ESMFold latent space by 128x (channel) and 8x (length) while preserving <2 Å accuracy.
Discrete compression created a tokenized all-atom structure vocabulary with high reconstruction accuracy.
CHEAP embeddings performed competitively on protein function and localization benchmarks.

Conclusions:

CHEAP embeddings offer mechanistic interpretability and a flexible representation of protein sequence and structure.
This approach democratizes access to large model representations.
CHEAP enables diverse downstream applications including protein generation, search, and prediction.