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Updated: May 17, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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United3D: a protein model quality assessment program that uses two consensus based methods.

Genki Terashi¹, Makoto Oosawa, Yuuki Nakamura

¹School of Pharmacy, Kitasato University, 5–9–1 Shirokane, Minato-ku, Tokyo 108–8641, Japan.

Chemical & Pharmaceutical Bulletin

|November 6, 2012

Summary

This summary is machine-generated.

United3D, a new protein model quality assessment program, accurately estimates protein structure quality. It demonstrated superior performance in identifying high-quality models during the CASP9 experiment.

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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

Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Accurate protein model quality assessment is crucial for template-based and ab initio modeling.
Existing methods require robust evaluation for reliable protein structure prediction.

Purpose of the Study:

To develop and evaluate United3D, a novel program for automated protein model quality assessment.
To assess United3D's performance in identifying high-quality protein models.

Main Methods:

United3D utilizes an optimized clustering method and a Cα atom contact-based potential.
It generates quality scores (Qscore) correlated with actual model quality (GDT_TS).

Main Results:

United3D achieved the lowest average loss of GDT_TS (5.3) in the CASP9 experiment.
It showed the best performance in identifying high-quality models among tested QA methods.
High average Pearson (0.93) and Kendall (0.68) correlation coefficients were observed between Qscore and GDT_TS.

Conclusions:

United3D is a valuable tool for selecting high-quality protein models from various prediction methods.
The program shows competitive performance against top-ranked QA methods.
United3D has the potential to enhance the accuracy of protein structure prediction.