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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 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 Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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Updated: Feb 24, 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

A Simple and Efficient Protein Structure Refinement Method.

Qianyi Cheng¹, InSuk Joung¹, Jooyoung Lee¹

¹Center for In Silico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study , Seoul 02455, Korea.

Journal of Chemical Theory and Computation

|August 12, 2017

Summary

This summary is machine-generated.

This study presents a novel protein structure refinement protocol using short molecular dynamics (MD) simulations. This method significantly improves protein structure prediction accuracy with reduced computational cost.

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Published on: December 30, 2016

Area of Science:

Computational structural biology
Biophysics
Molecular modeling

Background:

Accurate protein structure prediction is a major challenge in computational structural biology.
Previous methods relied on extensive millisecond molecular dynamics (MD) simulations for protein structure refinement.
The Critical Assessment of Structure Prediction (CASP) platform highlights the need for improved refinement techniques.

Purpose of the Study:

To develop a more efficient protein structure refinement protocol.
To reduce the computational resources required for accurate protein structure prediction.
To demonstrate systematic refinement using significantly less simulation time than previously reported.

Main Methods:

A novel refinement protocol combining short (5 ns) MD simulations with energy minimization.
Utilized an explicit solvent model.
Employed reduced positional and distance restraints compared to prior methods.

Main Results:

The protocol was tested on 54 CASP8-10 and 34 CASP11 refinement targets.
Achieved promising results in protein structure quality improvement.
Demonstrated systematic refinement using only nanosecond-scale MD simulations.

Conclusions:

A computationally efficient protein structure refinement protocol has been developed.
This method significantly reduces the simulation time and resources needed for refinement.
Accurate protein structure refinement is achievable within hours of desktop computing.