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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

Protein Organization

Protein and Protein Structure

Protein and Protein Structure

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.
A protein's shape is critical to its function. For example, an enzyme...

Protein and Protein Structures

Protein and Protein Structures

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Related Experiment Video

Updated: Apr 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

Comparative Protein Structure Modeling Using MODELLER.

Benjamin Webb¹, Andrej Sali

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

Current Protocols in Bioinformatics

|September 10, 2014

Summary

This summary is machine-generated.

Comparative modeling predicts protein 3-D structures using known related proteins. This guide details using MODELLER software for accurate protein structure prediction, including common errors and applications.

Keywords:

Modeller comparative modeling protein fold protein structure structure prediction

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

Protein structure determination is crucial for functional characterization.
Experimental structures are not always available.
Homology modeling offers a computational alternative for predicting protein 3-D structures.

Purpose of the Study:

To describe the process of comparative protein modeling.
To provide a guide for using the MODELLER software.
To illustrate modeling with a specific example, Trichomonas vaginalis lactate dehydrogenase (TvLDH).

Main Methods:

Comparative modeling based on sequence alignment to known structures (templates).
Key steps include fold assignment, target-template alignment, model building, and evaluation.
Utilizing the MODELLER software for model calculation.

Main Results:

Demonstration of comparative modeling workflow.
Discussion of potential errors and troubleshooting in the modeling process.
Successful application of MODELLER for TvLDH structure prediction.

Conclusions:

Comparative modeling with MODELLER is a viable approach for predicting protein structures.
Understanding the steps and potential pitfalls enhances model accuracy.
The described methods and software facilitate functional characterization of proteins lacking experimental structures.