• Software
    • DNASTAR LASERGENE
      Comprehensive Sequence Analysis
      • Lasergene Molecular Biology
      • Lasergene Genomics
      • Lasergene Protein
    • NOVA APPLICATIONS
      Protein Modeling
      • NovaFold AI
      • NovaFold
      • NovaFold Antibody
      • NovaDock
  • Workflows
    • Molecular Biology Workflows
      • Automated Virtual Cloning
      • Clone Sequence Verification
      • Gel Electrophoresis Simulation
      • Multiple Sequence Alignment
      • Pairwise Sequence Alignment
      • PCR Site-Directed Mutagenesis
      • PCR Primer Design
      • Phylogenetic Analysis
      • Plasmid Maps
      • Sanger Sequence Assembly
      • Sequence Editing and Annotation
  • Protein Analysis
    • Antibody Modeling
    • Antibody Phage Display
    • Epitope Prediction
    • Protein Docking
    • Protein Sequence Analysis
    • Protein Stability Prediction
    • Protein Structural Alignment
    • Protein Structure Analysis
    • Protein Structure Prediction
  • Genomics
    • Clinical Research
    • De Novo Genome Assembly
    • Mauve Genome Alignment
    • Metagenomic Assembly
    • Variant Analysis
    • Viral Genome Analysis
    • Whole Genome/Whole Exome
  • Transcriptomics
    • ChIP-Seq Data Analysis
    • De Novo Transcriptome Assembly
    • RNA-Seq Alignment
  • Services
    • Protein Services
    • Genomic Services
  • Pricing
  • Resources
    • Product Updates
    • Product Notifications
    • Blog
    • Educational Software Request
    • Documentation
    • Technical Requirements
      • File Formats
      • Licensing Options
  • Training
    • Help + Tutorials
    • Webinars
    • Technical Support Request
  • About
    • Careers
    • Distributors
    • Legal Information
    • Privacy Policy
  • Contact

QUESTIONS? CALL 866.511.5090

DOWNLOAD FREE TRIAL
SHOPPING CART
MY ACCOUNT
DNASTAR DNASTAR
  • Software
    • DNASTAR LASERGENE
      Comprehensive Sequence Analysis
      • Lasergene Molecular Biology
      • Lasergene Genomics
      • Lasergene Protein
    • NOVA APPLICATIONS
      Protein Modeling
      • NovaFold AI
      • NovaFold
      • NovaFold Antibody
      • NovaDock
  • Workflows
    • Molecular Biology
      • Automated Virtual Cloning
      • Clone Sequence Verification
      • Gel Electrophoresis Simulation
      • Multiple Sequence Alignment
      • Pairwise Sequence Alignment
      • PCR Site-Directed Mutagenesis
      • PCR Primer Design
      • Phylogenetic Analysis
      • Plasmid Maps
      • Sanger Sequence Assembly
      • Sequence Editing and Annotation
    • Protein Analysis
      • Antibody Modeling
      • Antibody Phage Display
      • Epitope Prediction
      • Protein Docking
      • Protein Sequence Analysis
      • Protein Stability Prediction
      • Protein Structural Alignment
      • Protein Structure Analysis
      • Protein Structure Prediction
    • Genomics
      • Clinical Research
      • De Novo Genome Assembly
      • Mauve Genome Alignment
      • Metagenomic Assembly
      • Variant Analysis
      • Viral Genome Analysis
      • Whole Exome/Genome Sequencing
    • Transcriptomics
      • ChIP-Seq Data Analysis
      • De Novo Transcriptome Assembly
      • RNA-Seq Alignment and Analysis
  • Services
    • Protein Services
    • Genomic Services
  • Pricing
  • Resources
    • Product Updates
    • Product Notifications
    • Blog
    • Educational Software Request
    • Documentation
    • Technical Requirements
      • File Formats
      • Licensing Options
  • Training
    • Help + Tutorials
    • Webinars
    • Technical Support Request
  • About
    • Careers
    • Distributors
    • Legal Information
    • Privacy Policy
  • Contact

PROTEIN SEQUENCE ANALYSIS

Comprehensive protein sequence analysis software integrated with tools for structural analysis and structure prediction. PRICING DOWNLOAD FREE TRIAL

Use Protean 3D for comprehensive protein sequence analysis in one easy-to-use application!

Protein sequence analysis is essential for studying and predicting protein function and structure, but often protein sequence analysis tools lack the visualization component necessary for interpretation, or they require additional tools for downstream analysis. The protein sequence analysis tools available in Protean 3D provide elegant graphical representations of the applied methods, making it simple to analyze biophysical properties, predict secondary structures such as B-cell epitopes, calculate surface probability, perform amino acid composition analysis, and more. What’s more, Protean 3D is a complete protein sequence analysis software package, meaning that after you analyze and annotate your protein sequence, you can immediately perform protein structure analysis, as well as predict protein structure, perform antibody modeling, or evaluate protein-protein docking interactions. Use Protean 3D to have everything you need for comprehensive protein sequence analysis in one easy-to-use application!

Human Calmodulin
The sequence analysis view in Protean 3D, showing biophysics and immunogenicity tracks applied to a protein sequence.

Protein sequence analysis in 4 simple steps

Protein Sequence Analysis Step 1

Step 1

Open a protein sequence or structure file

Protein Sequence Analysis Step 2

Step 2

Apply methods to analyze biophysical properties and secondary structure prediction

Protein Sequence Analysis Step 3

Step 3

Create annotations and customize appearance

Protein Sequence Analysis Step 4

Step 4

Export protein sequence analysis view for publication

computer

Learn more about Protein Sequence Analysis

Resources | Tutorials | FAQs | Citations | User Guide

PRICING
DOWNLOAD FREE TRIAL

Resources

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

PDF Icon

Lasergene Protein Overview

View Document

PDF Icon

Precise Predictions of Linear
B Cell Epitopes in Protean 3D

Read White Paper

Video Icon

How Can DNASTAR’s Protein Tools Help You?

Watch Webinar

Video Icon

Protean 3D Overview Webinar

Watch Webinar

Webinar Icon

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 sequence 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.

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.

Creating Features in Protean 3D

This quick tip video shows how to add custom annotations to a protein sequence or structure in Protean 3D.

Epitope Prediction Using the DNASTAR Method

This video demonstrates how to perform B-cell epitope prediction in Protean 3D.

Locating PROSITE Patterns on a Protein Sequence

See how to use the PROSITE method in Protean 3D to search for patterns and motifs on your sequence and compare them to your structure.

Identifying Protease Cleavage Sites Using Protean 3D

This video demonstrates how to view Protease cleavage sites on your protein sequence.

FAQs

What file types are supported for importing protein sequences for protein sequence analysis?

Protean 3D supports the following protein sequence file formats: *.aa, *.fap, *.fas, *.fasta, *.gp, *.gbk, *.sbd, and *.pro. Protean 3D also supports protein structure files from the Protein…

Protean 3D supports the following protein sequence file formats: *.aa, *.fap, *.fas, *.fasta, *.gp, *.gbk, *.sbd, and *.pro. Protean 3D also 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).

Show more

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.

Can I adjust the parameters used for the protein sequence analysis methods available in Protean 3D?

Yes. To change the parameters used for a protein sequence analysis method, first select the method from the Analysis view or from the Tracks panel. Then, edit the available parameters from the Options panel.

Can I change the appearance of the protein sequence analysis methods that I’ve applied to my protein sequence?

Yes. To change the appearance of a graph in the Analysis view, first select the graph by clicking on it, then edit the color and fill options from the Style panel.

How can I annotate my protein sequence?

To create an annotation on your protein sequence, select a portion of the sequence 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.

What hydropathy methods are available for protein sequence analysis?

Protean 3D offers three methods for creating hydropathy profiles for protein sequence analysis:

  • Hopp-Woods – predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity…

Protean 3D offers three methods for creating hydropathy profiles for protein sequence analysis:

  • Hopp-Woods – predicts protein antigenic determinants by searching protein sequences for the area of greatest local hydrophilicity. Hopp and Woods, 1981, make two assumptions in using hydrophilicity to find antigenic determinants: 1) antigenic determinants are usually found on regions with a high degree of exposure to solvents and 2) antigenic determinants commonly possess charged hydrophilic side chains. Each residue is assigned a hydrophilicity value and these values are averaged over a hexamer window.
  • Kyte-Doolittle – predicts regional hydropathy of proteins from their amino acid sequences, using the approach of Kyte and Doolittle, 1982. Hydropathy values are assigned for all amino acids and are then averaged over a user-defined window. The average is plotted at the midpoint of the window. Residue hydropathy assignments are derived from water-vapor transfer free energies and the interior-exterior distribution of residue side-chains.
  • Parker – uses the method of Parker et al., 1986, which is a hydrophilicity scale based on high-performance liquid chromatography retention times of model synthetic peptides. Hydrophilicity measures have been used extensively in the prediction of antigenic amino acid residues. The Parker method uses a modified Hopp-Woods algorithm together with a new set of hydrophilicity options.
Show more

What secondary structure prediction methods are available for protein sequence analysis?

Protean 3D offers four methods for predicting secondary structures:

  • Chou-Fasman – predicts secondary structure of proteins from the crystallographic structures of their amino acid sequences.
  • Deléage-Roux – predicts…

Protean 3D offers four methods for predicting secondary structures:

  • Chou-Fasman – predicts secondary structure of proteins from the crystallographic structures of their amino acid sequences.
  • Deléage-Roux – predicts secondary structure using the approach of Deléage and Roux, 1987. The method uses an independent prediction of the protein’s structural class to bias the prediction of its secondary structure.
  • Garnier-Robson – predicts protein structure from the amino acid sequence. The method examines the propensity of a given residue to exist in a certain structure.
  • Coiled Coil – predicts structures according to the formula of Lupas et al., 1991. You may use this track with the Transmembrane – Goldman-Engleman-Steitz track to predict transmembrane alpha helices.
Show more

How can I align my protein sequences?

You can easily perform multiple or pairwise protein sequence alignments in MegAlign Pro, part of Lasergene Molecular Biology.

Can I export an image of the protein sequence analysis view?

Yes. Protean 3D lets you export an image of the Analysis view for publication or collaboration. To do this, choose  File > Export Image > Analysis and save the image as a .pdf, .png, .jpg, or .pptx (Microsoft PowerPoint) file.

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.

Preparation of monoclonal antibodies against gamma-type phospholipase A2 inhibitors and immunodetection of these proteins in snake blood
Li, J., Xiong, Y., Sun, S. et al. J Venom Anim Toxins Incl Trop Dis 23, 37 (2017).

Development of Rift Valley fever (RVF) vaccine by genetic joining of the RVF-glycoprotein Gn with the strong adjuvant subunit B of cholera toxin (CTB) and expression in bacterial system
Ibrahim, Essam H., Taha, Ramadan, Ghramh, Hamed A., Kilany, Mona. Saudi Journal of Biological Sciences, Volume 26, Issue 7 (2019).

Identification and Pilot Evaluation of Salivary Peptides from Anopheles albimanus as Biomarkers for Bite Exposure and Malaria Infection in Colombia
Londono-Renteria, B.; Drame, P.M.; Montiel, J.; Vasquez, A.M.; Tobón-Castaño, A.; Taylor, M.; Vizcaino, L.; Lenhart, A.E. Int. J. Mol. Sci. 2020, 21, 691.

computer Ready to learn more? PRICING DOWNLOAD FREE TRIAL

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

Questions?

Our team of scientists is here to help!

CONTACT US

Or call (866) 511-5090

Scientists

Would you like to receive technical tips and special offers straight to your inbox?

  • Pricing
  • Software
  • Workflows
  • Resources
  • Training
  • About

Get a 14-Day free trial of our complete Lasergene package. Try before you buy!

FREE TRIAL DOWNLOAD

© 2022 — DNASTAR Privacy Policy

This website uses cookies to improve user experience and understand our web usage. By continuing to use our website, you consent to our use of cookies. Accept
Privacy & Cookies Policy
Necessary
Always Enabled