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Updated: Mar 21, 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

Calculating and scoring high quality multiple flexible protein structure alignments.

David W Ritchie¹

¹Inria Nancy - Grand Est, 54600 Villers-lès-Nancy, France.

Bioinformatics (Oxford, England)

|May 18, 2016

Summary

This summary is machine-generated.

This study introduces Kpax 5.0, an improved algorithm for flexible multiple protein structure alignments (MSAs). The new M-score measure demonstrates that accounting for structural flexibility yields higher quality MSAs.

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Area of Science:

Computational biology
Structural bioinformatics
Bioinformatics algorithms

Background:

Multiple protein structure alignments (MSAs) are crucial for understanding protein family relationships and homology modeling.
Existing rigid MSA algorithms have limitations, and few flexible MSA algorithms are available.
Incorporating backbone flexibility is key to overcoming these limitations.

Purpose of the Study:

To present novel improvements to the Kpax algorithm for calculating high-quality flexible MSAs.
To introduce a new Gaussian-based quality measure, the M-score, for MSAs.
To evaluate the performance of flexible MSAs against rigid ones.

Main Methods:

Novel improvements to the Kpax algorithm for flexible MSAs.
Introduction of the M-score, a Gaussian-based measure for MSA quality.
Large-scale evaluation using Homstrad, SABmark, and SISY benchmark sets.

Main Results:

Kpax 5.0 enables the calculation of high-quality flexible MSAs.
The M-score effectively measures MSA quality, outperforming RMSD-based measures.
Flexible alignment approaches, like Kpax and Matt, show superior performance over rigid methods like 3DCOMB.

Conclusions:

Accounting for structural flexibility is essential for accurate MSAs.
The M-score is a reliable metric for assessing MSA quality.
Kpax 5.0 offers a significant advancement in flexible MSA calculation.