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PROTEIN STRUCTURAL ALIGNMENT

Easily align two or more protein structures to identify, analyze, and visualize regions of similarity. PRICING DOWNLOAD FREE TRIAL

Use Protean 3D to easily perform protein structural alignments of entire macromolecular structures or selected regions.

Homologous proteins often have similar structures. Protein structural alignment software can be a valuable tool for identifying these similarities by comparing the shape and 3D conformation between structures. Protein structural alignment is also a valuable tool for comparing NovaFold predicted models to template structures from the Protein Data Bank. Protean 3D, part of Lasergene Protein, makes it easy to identify regions of similarity between two or more structures, independent of sequence similarity. Simply add your structure files or open your NovaFold results, and select from the TM-Align or jFATCAT rigid-body alignment algorithms. Following your protein structural alignment, evaluate RMSD values for aligned structures to determine their divergence from one another. Then, customize the rendering of your visualization in Protean 3D to prepare your protein structural alignment image for publication.

Protein structural alignment
Structural alignment of 3TA6:A (orange) and 7TIM:B (green), visualized in Protean 3D.

Protein structural alignment in 4 simple steps

Protein Structural Alignment Step 1

Step 1

Use File>Open Group or select structures from the NovaFold report to align

Protein Structural Alignment Step 2

Step 2

Select the chains you wish to align (or realign), then choose Structure>Align Structures

Protein Structural Alignment Step 3

Step 3

Evaluate RMSD values for aligned structures

Protein Structural Alignment Step 4

Step 4

View and change the rendering of your protein structural alignment for publication

computer

Learn more about Protein Structural Alignment

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on using protein structural alignment in Protean 3D.

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Lasergene Protein Overview

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High-Resolution in silico Protein Structure Prediction and Docking

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Modeling GPCR Structures in NovaFold

Read Case Study

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NovaFold and Custom Template Libraries

Read Blog Post

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From Protein Sequence to 3D Structure

Read Blog Post

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Protean 3D Overview Webinar

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How Can DNASTAR’s Protein Tools Help You?

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Tutorials

Watch one of our videos or check out our written tutorials to learn more about using Protean 3D protein structural alignment software.

Protein Structure Alignment in Protean 3D

In this video, we demonstrate how to align protein structures in Protean 3D in order to evaluate structural similarity.

Analyzing NovaFold Protein Structure Prediction Results

In this video, learn how to use the NovaFold report and analysis views to analyze your protein structure prediction models, including how to examine predicted ligand binding sites, align experimental structures to the prediction model, and analyze various statistics.

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.

FAQs

What file types are supported for protein structural alignments?

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).

How do I evaluate the results of my protein structural alignment?

The results of your protein structural alignment can be viewed in the Structure View of Protean 3D as a set of superimposed structures, where each alignment minimizes the root mean squared deviation (RMSD), or the average distance between atoms in superimposed structures. The RMSD values are also reported in the Details panel for a group of structures.

Can I export an image of my protein structural alignment for publication?

Yes. Protean 3D lets you export the actual structures within the alignment or an image of the protein structural alignment. To export the structures within your alignment, use File>Export Data > Export All Structures. To export an image of the protein structural alignment in .png, .jpg or .gif format, use File > Export Image > Structure.

What method does Protean 3D use for protein structural alignment?

Protean 3D uses the rigid-body alignment method for protein structural alignments, which determines the best alignment without allowing the structures to bend or twist. Available algorithms include TM-Align, Zhang and Skolnick (2005), and jFATCAT, Prlic et al. (2010), Ye et al. (2003).

Citations

Antibody mediated epitope mimicry in the pathogenesis of Zika virus related disease
Homan, E. Jane, Malone, Robert W., Darnell, Steven J., Bremel, Robert D. doi: https://doi.org/10.1101/044834 (2016).

Structural Determinants of the Interaction between the TpsA and TpsB Proteins in the Haemophilus influenzae HMW1 Two-Partner Secretion System
Grass, Susan, Rempe, Katherine A., St. Geme III, Joseph W. Journal of Bacteriology Apr 2015, 197 (10) 1769-1780; DOI: 10.1128/JB.00039-15.

Suppression of Drug Resistance Reveals a Genetic Mechanism of Metabolic Plasticity in Malaria Parasites
Guggisberg, Ann M., Frasse, Philip M., Jezewski, Andrew J., Kafai, Natasha M., Gandhi, Aakash Y., Erlinger, Samuel J., John, Audrey R. Odom. mBio Nov 2018, 9 (6) e01193-18; DOI: 10.1128/mBio.01193-18.

Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa
Szafranski, P. BMC Genomics 18, 269 (2017) doi:10.1186/s12864-017-3626-5.

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“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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