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Protein Organization

Protein Organization

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.
The primary structure of a protein is its amino acid sequence....

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: Oct 26, 2025

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Published on: March 10, 2021

Benchmarking of structure refinement methods for protein complex models.

Jacob Verburgt¹, Daisuke Kihara^1,2,3

¹Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.

|July 26, 2021

Summary

This summary is machine-generated.

This study benchmarks protein structure refinement methods for protein complex models. While improving native contacts is straightforward, backbone metrics like Root Mean Square Deviation remain challenging to enhance.

Keywords:

CAPRI protein complexes protein docking protein structure refinement protein-protein interaction

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Last Updated: Oct 26, 2025

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

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Published on: March 10, 2021

A Protocol for Computer-Based Protein Structure and Function Prediction

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

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Published on: October 15, 2018

Area of Science:

Computational Biology
Structural Biology
Biochemistry

Background:

Protein structure docking predicts the quaternary structure of protein complexes from individual tertiary structures.
Structure refinement is essential for computational protein docking models, correcting interface conformations.

Purpose of the Study:

To benchmark the performance of eight existing protein structure refinement methods.
To evaluate the effectiveness of refinement on protein complex models.

Main Methods:

Benchmarking of eight protein structure refinement algorithms.
Assessment of refinement efficacy using various metrics.

Main Results:

The fraction of native contacts between subunits is the most easily improved metric.
Backbone-dependent metrics, such as Root Mean Square Deviation, are more challenging to refine.

Conclusions:

Current refinement methods effectively improve native contact metrics in protein complex models.
Further development is needed to enhance backbone accuracy in refined protein complex structures.