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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.

Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

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Related Experiment Video

Updated: Jun 18, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Template-based protein modeling: recent methodological advances.

Pankaj R Daga¹, Ronak Y Patel, Robert J Doerksen

¹Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA.

Current Topics in Medicinal Chemistry

|November 26, 2009

Summary

This summary is machine-generated.

Protein structure prediction remains challenging, but template-based modeling advances offer solutions. This review covers recent progress in comparative protein modeling techniques for drug discovery.

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Last Updated: Jun 18, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Area of Science:

Computational biology
Structural biology
Drug discovery

Background:

Protein structure prediction is crucial but complex.
Template-based modeling is favored over ab initio methods.
Advancements in computational power aid protein modeling.

Purpose of the Study:

To review recent developments in comparative protein modeling.
To summarize progress in methodologies and understanding over the last three years.
To cover key aspects of the protein modeling pipeline.

Main Methods:

Review of literature on comparative protein modeling.
Analysis of advancements in homologue search and fold recognition.
Evaluation of techniques for secondary structure, loop, and side-chain prediction.
Assessment of model quality evaluation methods.

Main Results:

Significant progress in template-based modeling methodologies.
Improved accuracy in predicting protein three-dimensional structures.
Enhanced tools for various stages of comparative modeling.
Better methods for assessing the quality of predicted models.

Conclusions:

Comparative protein modeling has seen substantial advancements.
These improvements contribute significantly to drug discovery and computational biology.
Accurate protein structure prediction is becoming more attainable.