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# NOVAFOLD AI & NOVAFOLD AI-MULTIMER
Predict the structure of a single-chain protein using the AlphaFold 2 algorithm or
 >  > NovaFold AI and NovaFold AI-Multimer
## **NovaFold AI & NovaFold AI-Multimer**
Computational biology has come a long way in the past few years, and DNASTAR is leading the way in commercial . Both the prediction and analysis take place within the existing NovaCloud Services interface of .
### NovaFold AI handles even the most difficult single-chain folding problems
Our NovaFold AI protein structure prediction software enables you to seamlessly utilize the award-winning AlphaFold 2 method to predict the protein structure of an amino acid sequence, and then visualize and analyze your results. AlphaFold 2 was the top-ranked 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. In the most recent CASP Challenge, AlphaFold 2 achieved an average Z-score of 2.65 over 92 targets. The closest competitor achieved only 1.00 for the same number of targets. (See graph). AlphaFold 2 is extremely fast and typically finishes structure predictions in a few hours or less.
NovaFold AI is the first commercial software that can accurately predict even the most challenging protein structures:
• Membrane-bound proteins
NovaFold AI can also model multiple domains and their interactions with linkers, also known as multidomain protein structure prediction.
### NovaFold AI-Multimer for accurate prediction of multi-chained protein complexes
NovaFold AI-Multimer uses the AlphaFold-Multimer algorithm, an extension of AlphaFold 2 that was built by DeepMind to predict multiple chain protein complexes, also known as “multimers.” Compared to AlphaFold 2, AlphaFold-Multimer uses two additional metrics for evaluating prediction accuracy. Similarly to how NovaFold AI streamlines the process for AlphaFold 2, NovaFold AI-Multimer enhances the ease of setting up and running predictions with AlphaFold-Multimer. Setting up a prediction takes only a minute or two using a standard Windows or Mac computer.
AlphaFold-Multimer has not entered CASP under its own name. However, the top three performers in the multimer target class of CASP15 (2022), the most recent experiment for which results have been calculated, used the algorithm as a foundational element of their approaches. For this reason, AlphaFold-Multimer is widely considered to be the most accurate algorithm to date for predicting the quaternary structures of protein-protein complexes.
## Learn more about **NovaFold AI and NovaFold AI-Multimer**
## Resources
Please see our resources below for more information on NovaFold AI powered by AlphaFold 2.
Protein Structure Prediction with NovaFold AI
Protein Structure Prediction with NovaFold AI-Multimer
Accurate Protein Structure Prediction
NovaFold AI Help
## FAQs
**Do I need a Lasergene license to run NovaFold AI protein structure prediction software?**
Yes. A  license is required to run NovaFold AI or NovaFold AI-Multimer. , included in Lasergene Protein, provides the interface for running predictions and analyzing the results.
**Do you offer a free trial of NovaFold AI?**
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.
**What protein folding prediction method does NovaFold AI use?**
NovaFold AI uses the AlphaFold 2 artificial intelligence algorithm developed by . Of over 140 prediction algorithms tested in the most recent CASP challenge, AlphaFold 2 was not only the most accurate, but was an astonishing 2.65 times more accurate than the next-best algorithm. AlphaFold 2 creates distance maps between residues using a graph neural network based on its training data of ~100,000 protein structures. Part of its prediction process is to compare to existing templates in the included library. Unlike NovaFold, which uses the I-TASSER algorithm, NovaFold AI does not directly use templates to place atomic coordinates. However, NovaFold AI does use templates as part of the map building process.
**What protein folding prediction method does NovaFold AI-Multimer use?**
NovaFold AI-Multimer uses the AlphaFold-Multimer artificial intelligence algorithm developed by  as an extension of its AlphaFold2 algorithm. It is optimized to predict multiple chain protein complexes, also known as “multimers.” AlphaFold-Multimer was introduced in 2021, one year after AlphaFold2.
## To request access to NovaFold AI and/or NovaFold AI-Multimer, please complete the following form.
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# NOVAFOLD
Create highly accurate, 3D atomic models of proteins with unknown structures.
 >  > NovaFold
## NovaFold
Determining the 3D structure of a protein is important for understanding its function, but doing this in a lab through x-ray crystallography is expensive and cumbersome, especially when a large number of protein sequences are involved. That’s why we developed NovaFold, our  software. NovaFold utilizes the international award-winning I-TASSER algorithms developed by Professor Yang Zhang’s laboratory at the University of Michigan that combine threading and *ab initio* folding technologies to build accurate, full 3D atomic models of proteins with previously unknown structures. View and manipulate models of each predicted structure in , where you can effortlessly analyze structural data, predicted binding sites, and protein function.
* !
## Learn more about **NovaFold**
Please see our resources below for more information on NovaFold protein structure prediction software.
Use NovaFold to Predict a Protein Structure
Why Structure Prediction Matters
Modeling GPCR Structures in NovaFold
NovaFold and I-TASSER: A winning combination for protein structure prediction and analysis
Accuracy of NovaFold Protein Folding Predictions
NovaFold Help
* Quality models and useful insights
  *“Using the suite of DNASTAR programs, NovaFold, NovaFold Antibody, and NovaDock, I have generated functional models of antibody-antigen complexes from the component’s amino acid sequences. The quality of the models and the useful insights they generate more than justify the effort and computing time.”*
  Dr. Kurt Deshayes, Antibody Solutions
**Do I need a Lasergene license to run NovaFold protein structure prediction software?**
Yes. A  license is required to run NovaFold. , included in Lasergene Protein, provides the interface for running NovaFold predictions and analyzing the results.
**Do you offer a free trial of NovaFold?**
### What protein folding prediction method does NovaFold use?
NovaFold uses the I-TASSER algorithm developed by Professor Yang Zhang of the Department of Computational Medicine and Bioinformatics at the University of Michigan. This protein structure prediction…
NovaFold uses the I-TASSER algorithm developed by Professor Yang Zhang of the Department of Computational Medicine and Bioinformatics at the University of Michigan. This protein structure prediction algorithm utilizes a combination of threading and *ab initio* folding in .
Threading attempts to match portions of the query sequence to template sequences. The template sequences, and their experimentally solved structures, are part of the RCSB Protein Data Bank (PDB). *Ab initio* folding uses biophysical properties of the query sequence and simulations to determine the likely structure(s) of the protein.
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Ready to learn more?
# NOVAFOLD ANTIBODY
Predict highly accurate antibody models from sequence data in minutes.
 >  > NovaFold Antibody
## NovaFold Antibody
Creating accurate antibody models is crucial for antibody design and optimization. While many antibody modeling software tools rely solely on homology modeling, NovaFold Antibody’s unique algorithm generates models of antibodies and antibody fragments by combining homology modeling for framework regions and fragment-based or *ab initio* modeling for hypervariable loop regions, resulting in highly accurate . Simply provide sequences for the light chain, the heavy chain, or both, and NovaFold Antibody will return an annotated report that includes the predicted antibody models, as well as the highest likelihood heavy chain and light chain templates and annotations for locations of CDR loops. Easily view antibody modeling results with annotations in , part of , which allows you to fully customize the rendering to aid in visualization, or to prepare publication-quality images to export. Antibody modeling with NovaFold Antibody can also be used in conjunction with  to predict the structure and binding of antibody-antigen complexes.
## Learn more about **NovaFold Antibody**
Please see our resources below for more information on antibody structure prediction in NovaFold Antibody.
Antibody Modeling Workflow
How Can DNASTAR’s Protein Tools Help You?
Nova Applications on Mac: Bringing the Power of Protein Modeling to the Desktop
High Resolution Protein and Antibody Modeling with NovaFold and NovaFold Antibody
NovaFold Antibody Help
**Do I need a Lasergene license to run NovaFold Antibody?**
Yes. A  license is required to generate antibody models in NovaFold Antibody. , included in Lasergene Protein, provides the interface for running NovaFold Antibody predictions and analyzing the results.
**Do you offer a free trial of NovaFold Antibody?**
**What file types are supported for the light chain and heavy chain sequences required for antibody modeling?**
Light chain and heavy chain sequences can be added in the following protein file formats: .aa, .fap, .fas, .fasta, .gp, .gbk, .sbd, .pro.
### What is the prediction method used for antibody modeling by NovaFold Antibody?
The NovaFold Antibody algorithm utilizes a combination of homology modeling and *ab initio* loop prediction, resulting in highly accurate predictions. During modeling, NovaFold Antibody searches the input…
The NovaFold Antibody algorithm utilizes a combination of homology modeling and *ab initio* loop prediction, resulting in highly accurate predictions. During modeling, NovaFold Antibody searches the input sequence(s) against thousands of non-redundant protein antibody structures from PDB and finds the best template matches for the chain or complex.
During modeling, NovaFold Antibody gives particular consideration to the complementary determining region (CDR) loops, hypervariable regions of an antibody that react dominantly with an antigen. The three CDR loops on the heavy chain are known as H1, H2 and H3, while the three on the light chain are L1, L2 and L3. H3 is commonly the most important region in antigen binding. Due to its increased length and flexibility, it is also the most difficult to model. As such, NovaFold Antibody limits H3 loop modeling to fifteen or fewer residues, a length commonly seen in antibody modeling problems. Finally, NovaFold Antibody performs energy minimization calculations to construct the final predicted structure model for the antibody chain or complex. This entire process takes approximately 5-15 minutes on a standard workstation computer.