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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.
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Related Experiment Video

Updated: May 5, 2026

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins

Published on: June 4, 2021

Fingerprinting protein structures effectively and efficiently.

Xuefeng Cui¹, Shuai Cheng Li, Lin He

¹David R. Cheriton School of Computer Science, University of Waterloo, Ontario, Canada and Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.

Bioinformatics (Oxford, England)

|December 3, 2013

Summary

This summary is machine-generated.

ContactLib efficiently identifies similar protein structures by comparing local and remote similarities. This novel approach significantly improves accuracy over existing methods, making large-scale structural biology analysis feasible.

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Last Updated: May 5, 2026

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Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Assessing protein structure similarity is crucial in structural biology.
Existing alignment methods are computationally expensive for large datasets.
Current fragment-based methods may miss remote similarities.

Purpose of the Study:

To develop a fast and accurate method for protein structure comparison.
To overcome the limitations of existing structure alignment algorithms.
To improve the identification of both local and remote structural similarities.

Main Methods:

Introduced ContactLib, a novel approach using two contact libraries.
Represented protein structures using concise vectors derived from local and remote fragments.
Developed a combined hit-rate score for efficient similarity assessment.

Main Results:

ContactLib achieved a 0.960 area under the Receiver-Operating Characteristic curve on the SCOP30 dataset.
This represents a significant improvement over the previous best method, FragBag (0.747).
Incorporating remote contact information was critical for accurate neighbor retrieval.

Conclusions:

ContactLib offers a computationally efficient and highly accurate solution for protein structure comparison.
The method effectively identifies both local and remote structural similarities.
ContactLib facilitates large-scale analysis in structural biology.