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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 Organization

Protein Organization

Protein Organization

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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Updated: Mar 19, 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

Comparative Protein Structure Modeling Using MODELLER.

Benjamin Webb¹, Andrej Sali¹

¹University of California at San Francisco, San Francisco, California.

Current Protocols in Bioinformatics

|June 21, 2016

Summary

This summary is machine-generated.

This study explains comparative protein structure modeling, a method to predict protein 3D structures using known structures as templates. It details using MODELLER software and the ModBase database for accurate modeling, including error analysis.

Keywords:

MODELLER ModBase comparative modeling protein fold protein structure structure prediction

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Area of Science:

Computational Biology
Structural Bioinformatics
Protein Modeling

Background:

Comparative protein structure modeling leverages known protein structures (templates) to predict the 3D structure of a target protein sequence.
This process involves critical steps: fold assignment, target-template alignment, model building, and model evaluation.

Purpose of the Study:

To provide a comprehensive guide on calculating comparative protein models using MODELLER software.
To introduce the ModBase database for accessing and utilizing these models.
To discuss the four core steps of comparative modeling, common errors, and practical applications.

Main Methods:

Utilizing the MODELLER software package for comparative protein structure modeling.
Employing the ModBase database for model retrieval and analysis.
Detailed explanation of fold assignment, target-template alignment, model building, and evaluation procedures.

Main Results:

Demonstration of comparative modeling using lactate dehydrogenase from Trichomonas vaginalis (TvLDH) as a case study.
Guidance on downloading and installing the MODELLER software.
Discussion of frequently encountered errors and potential solutions in the modeling process.

Conclusions:

Comparative protein structure modeling with MODELLER and ModBase offers a robust approach for predicting protein structures.
Understanding the steps and potential pitfalls is crucial for successful model generation and application.
The described methods facilitate advancements in structural biology and drug discovery.