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Updated: Mar 14, 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

Modeling complexes of modeled proteins.

Ivan Anishchenko¹, Petras J Kundrotas¹, Ilya A Vakser^1,2

¹Center for Computational Biology, The University of Kansas, Lawrence, Kansas, 66047, USA.

|October 5, 2016

Summary

This summary is machine-generated.

Protein structure modeling is crucial but challenging. Template-based docking remains effective even with inaccurate protein models, offering a viable approach for reconstructing protein interactions.

Keywords:

interactome protein docking protein modeling protein recognition structure prediction

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Area of Science:

Structural biology
Computational biology
Bioinformatics

Background:

Experimental protein structures are scarce, especially for complexes.
Protein-protein interaction (PPI) modeling often uses less accurate, modeled protein structures.
Accurate PPI structural modeling is vital for understanding molecular mechanisms.

Purpose of the Study:

To systematically validate template-based and free docking methods.
To assess the impact of protein model accuracy on docking performance.
To evaluate docking success rates using CAPRI criteria.

Main Methods:

Tested 165 protein complexes using template-based and free docking.
Utilized protein models with varying structural accuracy (1-6 Å Cα RMSD).
Assessed docking predictions against CAPRI criteria.

Main Results:

Template-based docking achieved acceptable quality predictions even for inaccurate models (5-6 Å RMSD).
Docking success rates decreased significantly for models with >4 Å RMSD.
Template-based docking showed greater robustness to protein model inaccuracies than free docking.

Conclusions:

Existing protein docking methodologies are applicable to models with diverse accuracy levels.
Template-based docking is a reliable strategy for modeling protein-protein interactions, even with imperfect input structures.
This study provides insights into the Grand Challenge of modeling the interactome.