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## PROTEAN 3D
Explore macromolecular structure, motion, and function.
 >  > Protean 3D
## Protean 3D
Understanding the structure of a protein is critical to understanding protein function, but many protein analysis tools miss the crucial connection between analysis of protein structure and biophysical properties of the protein sequence. Protean 3D, the foundation of , rises above other protein analysis tools by offering flexible, rich 3D graphical representations of protein structures, incorporated with both  and ,  tools, and unmatched accuracy in predicting highly accurate, full atomic models of protein structures through integration with our .
* !
Learn more about **Protean 3D**
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## Protean 3D Workflows
\*Requires additional purchase of  predictions.
## Resources
Please see our resources below for more information on the protein visualization and analysis tools in Protean 3D.
How Can DNASTAR’s Protein Tools Help You?
How to Screen for Protein Hot Spots in Under 5 Minutes
How to perform PCR site-directed mutagenesis using Lasergene’s protein and primer design tools
Precise Predictions of Linear B Cell Epitopes in Protean 3D
Protean 3D Help
Protean 3D Tutorials
Results are second to none
*“Protean 3D is innovative. It allows me to 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
## FAQs
### Which Lasergene package includes Protean 3D?
Protean 3D is included in  as well as in the complete  package which includes all of the applications from , Lasergene Protein, and .
### Can I search NCBI databases online? Can I search local databases?
, , , , and  all offer the ability to do online sequence similarity searches in NCBI BLAST and text similarity searches in NCBI Entrez.
In addition, all but SeqBuilder Pro offer the ability to create and search local databases. First, use the Local Database Manager to upload local files and/or import sequences from NCBI, with over 30 databases to choose from. The manager can also be used to merge, expand, rename, and/or delete local databases. Local searches can then be done without Internet access and are a great way to ensure data security. In addition, local searches are 5–25x faster than online searches.
### Are Nova applications included with Protean 3D?
Each purchase of  (the package that includes Protean 3D), includes one free prediction for each of our Nova applications: , , and . Additional predictions may be purchased separately.
### What types of protein analysis can I do with Protean 3D?
Lasergene Protein’s Protean 3D application offers comprehensive protein  and , including , , and .
Lasergene Protein also includes access to , optional add-ons for , , and  interactions.
### What file types are supported for protein analysis in Protean 3D?
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  (\*.novafold, \*.antibody, \*.novadock).
## Compare DNASTAR Lasergene Packages
|  | | | | MOST POPULARDNASTAR Lasergene |
| --- | --- | --- | --- | --- |
|  | Lasergene Molecular Biology | Lasergene Genomics | Lasergene Protein |
| **Included Applications** |  |  |  |  |
| SeqBuilder Pro |  |  |  |  |
| SeqMan Ultra |  |  |  |  |
| MegAlign Pro |  |  |  |  |
| GeneQuest |  |  |  |  |
| GenVision |  |  |  |  |
| SeqNinja |  |  |  |  |
| SeqMan NGen |  |  |  |  |
| ArrayStar |  |  |  |  |
| GenVision Pro |  |  |  |  |
| Protean 3D (+1 prediction per Nova Application) |  |  |  |  |
| DNASTAR Navigator |  |  |  |  |
| **Supported Workflows** |  |  |  |  |
| Antibody Phage Display |  |  |  |  |
| Automated Virtual Cloning |  |  |  |  |
| Clone Sequence Verification |  |  |  |  |
| Gel Electrophoresis Simulation |  |  |  |  |
| Mauve Genome Alignment |  |  |  |  |
| Multiple Sequence Alignment |  |  |  |  |
| Pairwise Sequence Alignment |  |  |  |  |
| PCR Primer Design |  |  |  |  |
| PCR Site-Directed Mutagenesis |  |  |  |  |
| Phylogenetic Analysis |  |  |  |  |
| Plasmid Maps |  |  |  |  |
| Sequence Editing and Annotation |  |  |  |  |
| Sanger Sequence Assembly |  |  |  |  |
| ChIP-Seq Data Analysis |  |  |  |  |
| Clinical Research |  |  |  |  |
| *De Novo* Transcriptome Assembly |  |  |  |  |
| Large Scale Variant Analysis |  |  |  |  |
| Metagenomic Assembly |  |  |  |  |
| NGS *De Novo* Genome Assembly |  |  |  |  |
| RNA-Seq Alignment |  |  |  |  |
| Viral Genome Analysis |  |  |  |  |
| Whole Exome/Genome Sequencing |  |  |  |  |
| Antibody Modeling |  |  |  |  |
| Epitope Prediction |  |  |  |  |
| Protein Docking |  |  |  |  |
| Protein Sequence Analysis |  |  |  |  |
| Protein Stability Prediction |  |  |  |  |
| Protein Structural Alignment |  |  |  |  |
| Protein Structure Analysis |  |  |  |  |
| Protein Structure Prediction |  |  |  |  |
| **Integrates with** |  |  |  |  |
| DNASTAR Cloud Data Drive |  |  |  |  |
| DNASTAR Cloud Assemblies |  |  |  |  |
| NovaDock |  |  |  |  |
| NovaFold |  |  |  |  |
| NovaFold AI |  |  |  |  |
| NovaFold Antibody |  |  |  |  |
| **Pricing** Annual pricing starting at: | $699/year | $1,599/year  | $799/year  | $2,599/year |
|  | | | |  |
Ready to learn more?
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# NOVA APPLICATIONS
Revolutionary software for highly accurate protein structure prediction and modeling.
 >  > Nova Applications
## DNASTAR Nova Applications
## **NovaFold AI & NovaFold AI-Multimer**
 are  applications that enable you to seamlessly utilize the AlphaFold 2 or AlphaFold-Multimer methods to predict the protein structure of an amino acid sequence, and then visualize and analyze your results. AlphaFold 2 was the top-ranked single-chain protein structure prediction method in the  in 2020, significantly outperforming the other participating teams by determining the structure of proteins with accuracy comparable to laboratory experiments. AlphaFold-Multimer is an extension of the AlphaFold 2 algorithm that has been optimized to predict the structures of multichain protein complexes (multimers). This algorithm was the foundational element of the top three performers in the multimer target class of the  in 2022.  When you access these algorithms through NovaFold AI or NovaFold AI-Multimer, both structure prediction and analysis take place within the existing NovaCloud Services interface of .
## **NovaFold**
 is  software based on I-TASSER, the award-winning software package developed by Professor Yang Zhang’s laboratory at the University of Michigan. Utilizing the I-TASSER protein structure prediction algorithms that combine threading and *ab initio* folding technologies, NovaFold works with  to build accurate, full 3D atomic models of proteins with previously unknown structures.
## **NovaFold Antibody**
 software is specifically designed to  (Fv, Fab, VH, sdAb). The NovaFold Antibody algorithm utilizes a combination of homology modeling and *ab initio* loop prediction, resulting in highly accurate predictions that are analyzed within .
## **NovaDock**
 is a high-resolution  application that predicts atomic interactions between any two proteins. Simply provide your ligand and receptor sequence files, and NovaDock will predict the three-dimensional structure of the macromolecular complex for analysis in .
**How are Nova Applications sold?**
A license of  is required to run predictions with Nova Applications. NovaFold AI, NovaFold AI-Multimer, NovaFold, NovaFold Antibody, and NovaDock predictions can be . If you are interested in purchasing a bundle of predictions, please .
**What are the technical requirements for running Nova Applications?**
NovaFold, NovaFold Antibody and NovaDock can be run on the Cloud *or* locally on a server at your organization. NovaFold AI and NovaFold AI-Multimer are exclusively cloud-based. See our  for running Nova Applications locally.  is required to run all Nova Applications.
**Do you offer a free trial of Nova Applications?**
One prediction for each of our Nova Applications is included in our Lasergene free trial. We also offer free, no-obligation,  of any of our Nova Applications with one of our scientists on staff, tailored to your specific research objectives.
Questions?
Our team of scientists is here to help!
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