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Dali server: conservation mapping in 3D.

Liisa Holm¹, Päivi Rosenström

¹Institute of Biotechnology and Department of Biosciences, University of Helsinki, Helsinki, Finland. liisa.holm@helsinki.fi

Nucleic Acids Research

|May 12, 2010

Summary

The Dali web server provides protein structure comparison tools, aiding in the discovery of evolutionary relationships through structural analysis, complementing traditional sequence-based methods.

Area of Science:

Structural bioinformatics
Computational biology
Biochemistry

Background:

Protein structure comparison is crucial for understanding protein function and evolution.
Sequence analysis alone can miss evolutionary relationships detectable through structural similarities.

Purpose of the Study:

To present the Dali web server, a tool for comprehensive protein structure comparison.
To facilitate the analysis of structural neighborhoods and pairwise alignments.
To enable interactive exploration of structural conservation and ligand clustering.

Main Methods:

The Dali server utilizes the Dali program for comparing protein structures.
It accepts Protein Data Bank (PDB) identifiers or user-uploaded novel structures.
Results are presented in hyperlinked formats for interactive analysis.

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Main Results:

The Dali web server offers three distinct functionalities: structure comparison against PDB, browsing precomputed structural neighborhoods, and pairwise suboptimal alignment generation.
The interface is designed for ease of use, supporting interactive analysis of conserved residues and ligand clustering.
Structural comparison can reveal evolutionary insights missed by sequence analysis.

Conclusions:

The Dali web server is a valuable resource for protein structure comparison and analysis.
It enhances the discovery of evolutionary relationships through structural data.
The tool supports interactive exploration for deeper biological insights.