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Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Updated: May 28, 2026

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

STRIKE: evaluation of protein MSAs using a single 3D structure.

Carsten Kemena¹, Jean-Francois Taly, Jens Kleinjung

¹Bioinformatics and Genomics Program, Centre for Genomic Regulation and UPF, Aiguader, 88, 08003 Barcelona, Spain.

Bioinformatics (Oxford, England)

|November 1, 2011

Summary

We developed STRIKE, a novel method for evaluating protein sequence alignments using single structures. STRIKE accurately identifies the best alignment in 70% of cases, outperforming existing metrics.

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Area of Science:

Bioinformatics
Computational Biology
Structural Bioinformatics

Background:

Evaluating multiple protein sequence alignments is crucial but challenging.
Current methods often require multiple structures, which are not always available.
Accurate alignment is essential for understanding protein function and evolution.

Purpose of the Study:

To develop a method for assessing the relative accuracy of protein sequence alignments using only one structure.
To provide a more accessible tool for alignment quality evaluation.

Main Methods:

Developed STRIKE, a method utilizing single protein structures to compare alignment accuracy.
Validated STRIKE on standard datasets: BAliBASE, Homestrad, and Prefab.
Compared STRIKE's performance against Contact Accepted mutation and Blosum scores.

Main Results:

STRIKE successfully identifies the more accurate alignment in 70% of tested cases on average.
Performance improved to 79% for challenging datasets (e.g., BAliBASE RV11).
STRIKE demonstrated significantly higher discrimination capacity than existing metrics.

Conclusions:

STRIKE offers a robust and accurate solution for evaluating protein sequence alignments with limited structural data.
The method's effectiveness stems from refined contact definitions and improved substitution scoring.
STRIKE is available as open-source freeware, promoting wider adoption in biological research.