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Related Concept Videos

Protein Organization01:24

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 Models02:00

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.
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
Protein and Protein Structures02:15

Protein and Protein Structures

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 can...
Protein and Protein Structure02:15

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 can...

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Related Experiment Video

Updated: Jun 26, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Protein structure homology modeling using SWISS-MODEL workspace.

Lorenza Bordoli1, Florian Kiefer, Konstantin Arnold

  • 1Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH 4056 Basel, Switzerland.

Nature Protocols
|January 10, 2009
PubMed
Summary

Homology modeling builds protein 3D structures using related proteins as templates. SWISS-MODEL is a web-based system that generates and assesses these protein models efficiently.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Jun 26, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Homology modeling is a key computational method for predicting protein 3D structures.
  • Accurate protein structure models are crucial for understanding biological functions and drug discovery.

Purpose of the Study:

  • To describe the SWISS-MODEL workspace, an integrated web-based system for homology modeling.
  • To highlight the process of generating and assessing protein structure models using homology modeling.

Main Methods:

  • Utilizing SWISS-MODEL to search protein structure libraries for suitable templates based on sequence similarity.
  • Generating 3D protein models through sequence alignment with identified template structures.
  • Employing model quality assessment tools to evaluate the reliability of generated models.

Main Results:

  • SWISS-MODEL provides an integrated platform for automated homology modeling.
  • The system efficiently identifies templates and generates 3D protein models.
  • Quality assessment tools offer insights into model reliability.

Conclusions:

  • Homology modeling, as implemented in SWISS-MODEL, is the most accurate computational approach for generating reliable protein structures.
  • This method is widely applicable in various biological research areas.
  • The computational time for modeling is typically under 2 hours, excluding interpretation time.