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

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

Published on: July 16, 2017

BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles.

Dominik Gront¹, Maciej Blaszczyk, Piotr Wojciechowski

¹University of Warsaw, Faculty of Chemistry, Pasteura 1, 02-093 Warsaw, Poland. dgront@chem.uw.edu.pl

Nucleic Acids Research

|June 14, 2012

Summary

The BioShell Threader web server aids protein homology detection using 1D threading. It accurately assigns structural templates to protein domains, improving structural biology research.

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Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Protein homology detection is crucial for understanding protein function and evolution.
Existing methods often struggle with remote homology detection.
The BioShell package offers tools for biological sequence analysis.

Purpose of the Study:

To introduce the BioShell Threader, a web server for protein homology detection.
To enable the assignment of structural templates to query protein domains using 1D threading.
To improve the accuracy and reliability of protein structure prediction.

Main Methods:

Utilizes profile-to-profile alignment (1D threading) for homology detection.
Employs sequence profiles detailing sequence variability.
Incorporates secondary structure profiles predicting secondary structure probabilities.
Integrates three independent predictors to enhance prediction success rates.

Main Results:

The BioShell Threader server accurately assigns structural templates to protein domains.
Achieves nearly 80% accuracy in identifying the correct SCOP family for query sequences.
Demonstrates a high success rate in predicting structural templates.

Conclusions:

The BioShell Threader is a valuable tool for protein homology detection and structural template assignment.
The server enhances the capabilities of the BioShell package for structural bioinformatics.
Provides a reliable method for researchers to explore protein structure and function relationships.