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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 Organization

Protein Organization

Protein Folding

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Protein Folding

Protein Folding

Protein Folding

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Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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Updated: Apr 7, 2026

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

Effective protein model structure refinement by loop modeling and overall relaxation.

Gyu Rie Lee¹, Lim Heo¹, Chaok Seok²

¹Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea.

|July 15, 2015

Summary

This summary is machine-generated.

Protein structure refinement using ab initio methods can fix errors from template-based predictions. Overall structure relaxation consistently improves model quality, while loop modeling and multiple structure assessment offer additional benefits.

Keywords:

ANM CASP MD relaxation loop modeling refinement scoring function

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A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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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

Area of Science:

Computational biology
Structural bioinformatics
Protein modeling

Background:

Template-based protein structure prediction methods can introduce errors, especially with low sequence similarity.
Sequence variations (insertions/deletions) can lead to missing structural information in local regions like loops.
Ab initio structure refinement methods are crucial for improving accuracy in regions deviating from templates.

Purpose of the Study:

To evaluate the effectiveness of different ab initio structure refinement strategies.
To assess methods including overall structure relaxation, loop modeling, and multi-structure quality assessment.
To identify optimal refinement approaches for protein structure prediction.

Main Methods:

Testing three distinct ab initio refinement techniques in the CASP11 experiment.
Implementing overall structure relaxation for global model improvement.
Utilizing loop modeling for specific sequence variation regions.
Employing quality assessment of multiple initial structures for further refinement.

Main Results:

Overall structure relaxation consistently enhanced protein model quality.
Loop modeling proved most effective for high-quality initial models (GDT-HA >60).
Refinement using multiple initial structures yielded minor improvements, highlighting potential energy function limitations.

Conclusions:

Ab initio structure refinement, particularly overall relaxation, is a valuable approach to enhance protein model accuracy.
The utility of loop modeling is contingent on the quality of the initial protein model.
Further development of energy functions may be necessary for advanced refinement techniques.