Protein Structure Analysis Workflow

Use Protean 3D for complete protein structure analysis in one user-friendly application!

Understanding the structure of a protein is critical to understanding protein function, but many protein structure analysis tools available today lack the high-quality visualization component necessary for effective analysis and miss the crucial connection between analysis of protein structure and biophysical properties of the protein sequence. Protean 3D, part of Lasergene Protein, removes these challenges by creating beautiful, flexible, rich graphical representations of your protein and providing full integration with protein sequence analysis and structure prediction tools in a single application. Our protein structure analysis tools make it effortless to analyze your protein structure for regions of interest or to introduce a mutation and see the impact on the protein structure. Infinite possibilities for visualizing the three-dimensional protein structure provide an uncomplicated means of producing publication-quality images. Use Protean 3D to have everything you need for comprehensive protein structure analysis in one user-friendly application!

Structure of nucleoside diphosphate kinase (4HR2) visualized in Protean 3D's structure view.

Protein structure analysis in 4 simple steps

Step 1

Open protein structure file locally or directly from the Protein Data Bank.

Step 2

Utilize integrated protein sequence analysis tools to highlight regions of interest on the protein structure

Step 3

Introduce mutations to see the impact on protein structure, apply molecular and solvent accessible surfaces, or scan for hot spots that contribute to fold stability.

Step 4

Change the rendering, orientation and lighting on your structure to prepare it for publication.

Learn more about Protein Structure Analysis

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on using the protein structure analysis tools in Protean 3D.

Lasergene Protein Overview

View Document

Protean 3D Overview Webinar

Watch Webinar

Identifying Candidate Variants and Their Effects on Protein Structure

View Poster

Structure-guided molecular cloning for improving site-directed mutagenesis and stability in protein design

View Poster

Modeling GPCR Structures in NovaFold

Read Case Study

High-Resolution in silico Protein Structure Prediction and Docking

View Poster

NovaFold and Custom Template Libraries

Read Blog Post

From Protein Sequence to 3D Structure

Read Blog Post

Tutorials

Watch one of our videos or check out our written tutorials to learn more about using the protein structure analysis tools in Protean 3D.

Lasergene Protein Overview

This video gives an overview of Lasergene Protein, consisting of Protean 3D, plus the optional services NovaFold, NovaFold Antibody and NovaDock.

Changing Rendering Styles to Highlight Features of Interest

This video demonstrates how Protean 3D makes it easy to highlight features of interest in your structure by changing rendering styles.

Creating Surfaces and Adjusting Lighting on Structures in Protean 3D

In this video, we show you how to create surfaces around your macromolecular structures in Protean 3D. We also show how to adjust lighting to optimize the structure view for presentation.

Protean 3D's Analysis View

Protean 3D’s Analysis View enables you to evaluate secondary structural characteristics of a sequence using a variety of known bioinformatics prediction methods with customizable parameters.

FAQs

What file types are supported for protein structure analysis?

Protean 3D supports protein structure files from the Protein Data Bank (*.pdb, *.ent, *.pdb.gz, *.ent.gz, *.zip, *.txt), as well as structure files created by Protean 3D (*.structure) or one of our Nova Applications (*.novafold, *.antibody, *.novadock).

Can I customize the appearance of my protein structure?

Yes. Protean 3D offers unmatched flexibility in customizing the appearance of your protein structure. First select the molecule(s) you wish to edit, then access the Styles panel where you can adjust the rendering, color, and lighting for your protein structure.

How can I annotate my protein structure?

To create an annotation on your protein structure, first select the structural element you wish to annotate and then choose Features>New Feature. The Options area of the Features panel automatically becomes populated with a default name, as well as information about the molecule and endpoints of the feature.

How do I apply protein sequence analysis methods to analyze biophysical properties and predict secondary structures?

To analyze biophysical properties and predict secondary structures on your protein sequence, select the desired method from the Tracks panel, located by default on the right side of the Protean 3D window. The Analysis view displays a graphical representation of all of the tracks that have been applied to the active sequence or structure.

How can I identify similarities between multiple protein structures?

You can use Protean 3D to easily perform protein structural alignments of entire macromolecular structures or selected regions. Simply add your structure files or open your NovaFold results, then select the chains you wish to align and choose Structure>Align Structures. Following your protein structural alignment, evaluate RMSD values for aligned structures to determine their divergence from one another.

What types of surfaces can I create on my protein structure?

Protean 3D allows you to easily create molecular and solvent accessible surfaces around your structure to clearly view structural elements of interest relative to the protein surface. To apply a molecular surface or a solvent accessible surface, click on the Create a surface button, located in the Surfaces area of the Explorer panel. Choose the surface style and speed from the drop down list provided to create a surface for the current selection, or for all chains, if nothing is selected.

How can I see the impact of a mutation on my protein structure?

Protean 3D includes protein stability prediction tools which allow you to make changes at the residue-level on a protein structure and predict whether these changes are likely to be stabilizing or destabilizing compared to the original structure. To introduce a variant, first select the residues you wish to mutate from the Sequence view . Then, choose Modeling > Protein Design > Create Variant With > Selection. Use the Substitute drop-down menus to select a different amino acid for each position of interest and then click Run. In most cases, protein mutation stability predictions are available in a matter of seconds.

Does Lasergene Protein include software for protein structure prediction?

Yes. Lasergene Protein includes access to our Nova Applications for protein structure prediction, antibody modeling, and protein-protein docking interactions.

What options are available for exporting my protein structure?

Protean 3D allows you to export the protein structure itself or an image of the structure for publication. To export your protein structure as a .pdb or .cif file, use Export Data > Export Structure. To export an image of your protein structure in .png, .jpg or .gif format, use File > Export Image > Structure.

Citations

The Photorhabdus asymbiotica virulence cassettes deliver protein effectors directly into target eukaryotic cells
Vlisidou, Isabella et al. eLife vol. 8 e46259. 17 Sep. 2019, doi:10.7554/eLife.46259.

A Repetitive DNA Element Regulates Expression of the Helicobacter pylori Sialic Acid Binding Adhesin by a Rheostat-like Mechanism
Åberg A, Gideonsson P, Vallström A, et al. PLoS Pathog. 2014;10(7):e1004234. Published 2014 Jul 3. doi:10.1371/journal.ppat.1004234.

Immunotopological Analysis of the Treponema denticola Major Surface Protein (Msp)
Godovikova, Valentina, et al. Journal of Bacteriology Dec 2018, 201 (2) e00528-18; DOI: 10.1128/JB.00528-18.

Evidence of a Mild Mutator Phenotype in Cambodian Plasmodium falciparum Malaria Parasites
Lee, Andrew H., Fidock, David A. PloS one vol. 11,4 e0154166. 21 Apr. 2016, doi:10.1371/journal.pone.0154166.

PLA2R-associated membranous glomerulopathy is modulated by common variants in PLA2R1 and HLA-DQA1 genes
Saeed, M., Beggs, M., Walker, P. et al. Genes Immun 15, 556–561 (2014). https://doi.org/10.1038/gene.2014.50

Results are second to none

“Protean 3D is innovative. It allows me answer questions that were not explored previously, and the in-silico accuracy of results are second to none as determined by comparing with in-vitro techniques.”

Alebachew Messele, Addis Ababa University

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