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Protein and Protein Structure

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Related Experiment Video

Updated: Jan 22, 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

Structural modeling of protein complexes: Current capabilities and challenges.

Justas Dapkūnas¹, Kliment Olechnovič¹, Česlovas Venclovas¹

¹Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.

|July 12, 2019

Summary

This summary is machine-generated.

Computational modeling of protein complexes is advancing, with template-based methods showing success. However, free docking requires further improvements for accurate protein structure prediction.

Keywords:

CAPRI CASP binding sites docking homology modeling model quality assessment protein complexes protein-protein interactions scoring template-based modeling

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Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Protein complex structures are crucial for understanding biological functions.
Computational methods are vital for modeling these complex structures.
The Critical Assessment of protein Structure Prediction (CASP) experiment evaluates progress in this field.

Purpose of the Study:

To assess computational protein complex modeling capabilities during CASP13.
To identify key factors influencing the accuracy of protein complex modeling.
To evaluate the effectiveness of template-based, docking, and hybrid approaches.

Main Methods:

Applied template-based modeling, free docking, and hybrid techniques for protein complex modeling.
Utilized homology modeling when protein complex templates were available.
Combined template-based modeling with docking when partial templates were identified.

Main Results:

Successfully modeled 27 out of 42 multimers with high quality using available templates.
Template-based modeling with homology or docking achieved reasonable accuracy.
Free docking showed limited success, with challenges in subunit orientation and interface contacts.

Conclusions:

Template availability significantly impacts the accuracy of protein complex modeling.
Hybrid approaches combining templates and docking show promise.
Improvements in monomer model quality and scoring functions are needed for free docking.