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Updated: Feb 15, 2026

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

Fragger: a protein fragment picker for structural queries.

Francois Berenger¹, David Simoncini², Arnout Voet³

¹System Cohort Division, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.

|May 28, 2019

Summary

This summary is machine-generated.

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Fragger software enables efficient querying of 3D protein fragment databases, supporting custom datasets and structural gaps. This tool aids protein design and structural bioinformatics tasks by facilitating fragment selection and comparison.

Area of Science:

Structural Bioinformatics
Computational Biology
Protein Science

Background:

Protein modeling and design frequently involve querying structural databases with fragments.
Existing methods may lack flexibility in handling custom PDB subsets or unpublished structures.
User-specific requirements necessitate advanced tools for managing and querying 3D protein fragments.

Purpose of the Study:

To introduce Fragger, a novel software for creating and querying 3D protein fragment databases.
To provide a flexible tool for protein design and structural bioinformatics tasks.
To enable efficient searching and analysis of protein structural fragments.

Main Methods:

Fragger allows the creation of databases from any set of Protein Data Bank (PDB) files.

Keywords:

fragments database protein design protein fragments structural query triangular inequality

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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It supports fragments of all lengths and queries with potential structural gaps.

Sequence constraints can be applied using regular expressions of amino acid codes.

Main Results:

Fragger efficiently searches fragment databases based on query fragments and distance thresholds.
Matching fragments are ranked by their distance to the query.
Includes a high-throughput tool for computing backbone Root Mean Square Deviation (RMSD) between fragments.

Conclusions:

Fragger offers a robust solution for managing and querying 3D protein fragments.
The software is well-suited for protein design, loop grafting, and other structural bioinformatics applications.
Its capabilities enhance the efficiency and flexibility of structural analysis and design workflows.