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Protein and Protein Structure

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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.
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Related Experiment Video

Updated: Jan 31, 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

Multiple protein structure alignment at scale with FoldMason.

Cameron L M Gilchrist^1,2, Milot Mirdita¹, Martin Steinegger^1,3,4,5

¹School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.

Science (New York, N.Y.)

|January 29, 2026

Summary

This summary is machine-generated.

FoldMason is a new computational tool for aligning protein structures, enabling faster and more accurate analysis of distantly related proteins. This advance aids in understanding protein evolution and function, even with limited sequence data.

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Area of Science:

Structural bioinformatics
Computational biology
Protein structure analysis

Background:

Protein structure conservation extends beyond sequence, necessitating multiple structural alignment (MSTA) for analyzing distantly related proteins.
Advances in computational protein structure prediction generate vast datasets, demanding efficient and accurate MSTA methods.

Purpose of the Study:

To introduce FoldMason, a novel progressive MSTA method designed for high-throughput analysis of large protein structure datasets.
To evaluate FoldMason's speed and accuracy against existing state-of-the-art MSTA methods.

Main Methods:

FoldMason employs a progressive alignment strategy, utilizing pairwise structural aligners Foldseek and TM-align.
The method was tested on large-scale datasets, including Flaviviridae glycoproteins, to assess its performance.
Confidence scores and interactive visualizations are integrated into the FoldMason workflow.

Main Results:

FoldMason achieves alignment quality comparable to or exceeding current state-of-the-art MSTA methods.
The method demonstrates a significant speed improvement, being two orders of magnitude faster than existing tools.
FoldMason's multiple structural alignments facilitate robust phylogenetic analysis, extending beyond the 'twilight zone' of sequence similarity.

Conclusions:

FoldMason provides essential speed and accuracy for large-scale protein structure analysis, crucial in the era of accurate structure prediction.
The tool supports phylogenetic analysis of distantly related proteins, enhancing evolutionary studies.
FoldMason is a free, open-source software, promoting accessibility for the scientific community.