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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

PhyreStorm: A Web Server for Fast Structural Searches Against the PDB.

Stefans Mezulis¹, Michael J E Sternberg¹, Lawrence A Kelley¹

¹Structural Bioinformatics Group, Imperial College London, London SW7 2AZ, United Kingdom.

Journal of Molecular Biology

|November 1, 2015

Summary

PhyreStorm rapidly compares protein structures against the Protein Data Bank (PDB), enabling biologists to explore protein relationships. This tool enhances structural biology research by providing fast and accurate structural alignments.

Keywords:

TM-align one-vs-many protein structural alignment structural search

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Area of Science:

Structural Biology
Bioinformatics
Evolutionary Biology

Background:

Identifying structurally similar proteins offers biological insights.
Protein structure alignment is crucial in structural and evolutionary biology.
Bioinformatic tools are essential for exploring protein structure relationships.

Purpose of the Study:

To introduce PhyreStorm, a web server for rapid and comprehensive protein structure comparisons.
To provide biologists, including those less experienced in bioinformatics, with a tool for exploring protein structure relationships.
To facilitate structural analysis beyond sequence-based methods.

Main Methods:

PhyreStorm compares query proteins against the Protein Data Bank (PDB).
The PDB is partitioned into similar structures to optimize alignment searches.
The server utilizes an intuitive user interface for accessibility.

Main Results:

PhyreStorm achieves rapid structural comparisons, typically under 60 seconds.
It significantly reduces the number of required alignments by partitioning the PDB.
The server identifies 93±2% of highly similar structures (TM-score>0.7).

Conclusions:

PhyreStorm offers a powerful and efficient tool for protein structure comparison.
It democratizes access to advanced structural analysis for a broader range of biologists.
The server enhances the exploration of protein structure-function and evolutionary links.