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Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Updated: May 28, 2026

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

Published on: October 13, 2022

An automatic method for CASP9 free modeling structure prediction assessment.

Qian Cong¹, Lisa N Kinch, Jimin Pei

¹Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.

Bioinformatics (Oxford, England)

|October 14, 2011

Summary

This summary is machine-generated.

A new automatic scoring system, Quality Control Score (QCS), objectively assesses protein structure prediction models. QCS shows high agreement with manual inspection and outperforms other automated methods in identifying high-quality protein models.

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Area of Science:

Computational biology
Structural bioinformatics
Protein structure prediction

Background:

Manual inspection is the standard for Critical Assessment of Protein Structure Prediction (CASP) free modeling (FM) but is subjective and time-consuming.
Existing automated methods struggle to differentiate models of similar quality and lack reproducibility.

Purpose of the Study:

To develop an automated scoring system that mimics manual inspection for objective and reproducible protein structure model assessment.
To improve the accuracy and reliability of protein structure prediction evaluation.

Main Methods:

Developed the Quality Control Score (QCS), an automatic, superimposition-independent method.
QCS analyzes both global and local structural features, prioritizing global topology.
Applied QCS to CASP9 FM targets.

Main Results:

QCS demonstrated the best agreement with Manual Inspection Scores among automated methods evaluated in CASP.
QCS showed strong correlation with other scoring methods like Global Distance Test Total Score (GDT_TS) and Contact Score (CS).
QCS successfully identified high-quality models that were overlooked by GDT_TS.

Conclusions:

QCS provides an objective, reproducible, and accurate method for assessing protein structure prediction models.
The developed QCS method enhances the evaluation of protein structure predictions, particularly in the challenging FM category.