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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 Organization

Protein Organization

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 and Protein Structures

Protein and Protein Structures

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

Conservation of Protein Domains

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Updated: Jan 15, 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

Protein foundation models: a comprehensive survey.

Hao Xu¹, Liangjie Li¹, Sangyu Pan¹

¹Bioinformatics Center of AMMS, Beijing, 100850, China.

Science China. Life Sciences

|January 13, 2026

Summary

Protein foundation models (pFMs) are powerful AI tools transforming protein science. This review explores their development, diverse applications in biology and medicine, and future potential for bioengineering and therapeutics.

Keywords:

AI virtual cells autoencoding models autoregressive models diffusion models flow matching models protein foundation model

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Last Updated: Jan 15, 2026

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Area of Science:

Computational Biology
Protein Science
Artificial Intelligence in Biology

Background:

Protein foundation models (pFMs) leverage deep learning on large datasets.
They learn generalizable protein patterns for prediction and generation.
Multimodal data (sequences, structures, functions, interactions) are crucial.

Purpose of the Study:

To provide a comprehensive review of pFM developments.
To explore applications, challenges, and future prospects of pFMs.
To serve as a guide for computational biologists and experimentalists.

Main Methods:

Systematic examination of multimodal protein datasets.
Exploration of various pFM architectures (autoencoding, autoregressive, diffusion, flow matching).
Review of applications in fundamental research, protein engineering, and biomedicine.

Main Results:

pFMs demonstrate versatility and significant impact across biological research.
Key challenges include data limitations, evaluation, and interpretability.
Promising future directions involve modeling protein dynamics and interactions.

Conclusions:

pFMs are pivotal tools advancing protein science.
Addressing challenges will unlock next-generation bioengineering and therapeutics.
Integrated virtual cell systems represent a future frontier.