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Related Experiment Video

Updated: Nov 11, 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

ZEAL: protein structure alignment based on shape similarity.

Filip Ljung¹, Ingemar André¹

¹Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund SE-22100, Sweden.

Bioinformatics (Oxford, England)

|March 27, 2021

Summary

This summary is machine-generated.

ZEAL is a new tool that superposes protein structures by their surface shape, outperforming other methods. It helps compare divergent proteins and reveals functional relationships, especially for DNA-binding proteins.

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Published on: July 14, 2015

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Traditional protein structure superimposition relies on Cartesian coordinates, limiting comparisons of distantly related proteins.
Protein function is often dictated by surface shape, making shape-based comparisons crucial for understanding biological relationships.

Purpose of the Study:

To introduce ZEAL, an interactive tool for superposing protein structures based on molecular surface shape resemblance.
To evaluate ZEAL's performance against existing methods and explore its utility in identifying functional relationships.

Main Methods:

Utilized 3D Zernike-Canterakis functions to represent protein molecular surfaces.
Developed ZEAL as an interactive tool with online and standalone versions.
Benchmarked ZEAL against other shape-based and coordinate-based superimposition methods.

Main Results:

ZEAL demonstrated superior performance in shape-based superposition compared to other methods for proteins with similar folds.
ZEAL alignments showed comparable quality to TM-align for fold-similar proteins.
ZEAL successfully identified substantial surface-shape correspondence for proteins with limited sequence and fold similarity, where coordinate-based methods fail.
Identified significant correlations between global surface shape similarity and protein function, particularly for DNA-binding proteins.

Conclusions:

ZEAL provides an effective method for comparing protein structures based on surface shape, enabling analysis of divergent proteins.
Shape-based superimposition using ZEAL can reveal evolutionary relationships and functional similarities missed by traditional methods.
ZEAL is a valuable tool for studying the link between protein surface shape and function, with implications for discovering novel protein relationships.